EHR Pricing Explained: Hidden Costs and Add-ons in 2026

EHR pricing is notoriously confusing. A system advertised at "$99/month" can easily cost $300-500/month once you add essential features. Understanding the real cost before you commit can save you thousands of dollars and prevent buyer's remorse.

This guide breaks down every pricing model, hidden fee, and add-on cost so you can budget accurately and choose the right EHR for your practice.

Quick Answer

EHR systems use four main pricing models: (1) Per-provider monthly ($50-500/month), (2) Percentage of collections (3-8%), (3) Per-claim fees ($0.50-3.00), and (4) Flat-rate unlimited ($99-300/month). Hidden costs include setup fees ($500-5,000), training ($200-2,000), data migration ($500-3,000), integrations ($50-200/month), and per-feature add-ons. The true cost is typically 40-60% higher than the advertised base price. ClinikEHR offers transparent flat-rate pricing with no hidden fees or per-claim charges.

EHR Pricing Models Explained

Model 1: Per-Provider Monthly Subscription

How It Works:

• Pay monthly fee per provider
• Typically tiered by features
• Most common model

Typical Pricing:

• Basic: $50-150/month per provider
• Standard: $150-300/month per provider
• Premium: $300-500/month per provider

What's Usually Included:

• Core EHR functionality
• Basic scheduling
• Clinical notes
• Limited support

What Costs Extra:

• E-prescribing ($20-50/month)
• Billing features ($50-100/month)
• Telehealth ($30-75/month)
• Patient portal ($20-40/month)
• Advanced reporting ($30-60/month)
• API access ($50-150/month)

Example Real Cost:

Advertised: $199/month per provider
+ E-prescribing: $30/month
+ Billing: $75/month
+ Telehealth: $50/month
+ Patient portal: $25/month
+ Support upgrade: $40/month
= Actual Cost: $419/month per provider

Best For: Solo practitioners and small practices with predictable needs

Watch Out For:

• Per-provider fees add up quickly
• Feature add-ons can double the cost
• Annual contracts with penalties

Model 2: Percentage of Collections

How It Works:

• Pay 3-8% of all collected revenue
• Includes full revenue cycle management
• Vendor handles billing and collections

Typical Pricing:

• Self-service: 3-5% of collections
• Full-service: 5-8% of collections

What's Usually Included:

• Complete EHR system
• Billing and coding
• Claims submission
• Payment posting
• Denial management
• Patient statements

What Costs Extra:

• Setup and training
• Data migration
• Custom reports
• Additional users
• Premium support

Example Real Cost:

Practice collecting $30,000/month
× 6% collection fee
= $1,800/month ($21,600/year)

Compare to flat-rate at $300/month ($3,600/year)
Difference: $18,000/year

Best For: Practices wanting full billing outsourcing

Watch Out For:

• Costs scale with revenue (can get expensive)
• Less control over billing process
• Difficult to switch vendors
• May incentivize aggressive billing

Model 3: Per-Claim Fees

How It Works:

• Base monthly fee + per-claim charges
• Pay for each claim submitted
• Common in billing-focused systems

Typical Pricing:

• Base fee: $50-200/month
• Per claim: $0.50-3.00 per claim

Example Real Cost:

Base fee: $99/month
+ 100 claims × $1.50 per claim = $150/month
= Total: $249/month

High-volume practice:
Base fee: $99/month
+ 400 claims × $1.50 per claim = $600/month
= Total: $699/month

Best For: Very low-volume practices (under 50 claims/month)

Watch Out For:

• Costs unpredictable month-to-month
• Penalizes practice growth
• Can become very expensive
• Hidden in fine print

Model 4: Flat-Rate Unlimited

How It Works:

• One price for unlimited users/claims
• All features included
• Predictable budgeting

Typical Pricing:

• Solo/Small: $99-200/month
• Group Practice: $200-500/month
• Enterprise: Custom pricing

What's Usually Included:

• All core features
• Unlimited users
• Unlimited claims
• All integrations
• Standard support

What Costs Extra:

• Premium support (sometimes)
• Custom development
• Advanced training

Example Real Cost:

Advertised: $99/month
+ Setup: $0 (included)
+ Training: $0 (included)
+ All features: $0 (included)
= Actual Cost: $99/month

Best For: Practices wanting predictable costs and full features

Watch Out For:

• Ensure "unlimited" truly means unlimited
• Check what's actually included
• Verify no hidden per-claim fees

ClinikEHR Model: Flat-rate with all features included, no per-claim fees

Hidden Costs Breakdown

Setup and Implementation Fees

What They Cover:

• System configuration
• Data import
• User setup
• Initial training

Typical Costs:

• Self-service: $0-500
• Assisted setup: $500-2,000
• Full implementation: $2,000-5,000
• Enterprise: $5,000-20,000+

Questions to Ask:

• Is setup included or extra?
• What does setup include?
• Can I do it myself to save money?
• Are there ongoing setup fees?

ClinikEHR: Free setup included in all plans

Training Costs

What's Included:

• Initial training sessions
• Documentation and guides
• Video tutorials
• Ongoing support

Typical Costs:

• Self-paced: Free-$200
• Live group training: $200-1,000
• One-on-one training: $500-2,000
• On-site training: $2,000-5,000+

Hidden Costs:

• Staff time during training
• Reduced productivity during transition
• Retraining for new staff

Budget: $500-2,000 for comprehensive training

Data Migration Fees

What's Involved:

• Exporting data from old system
• Formatting for new system
• Importing and verification
• Testing and validation

Typical Costs:

• Simple migration: $500-1,500
• Complex migration: $1,500-3,000
• Enterprise migration: $3,000-10,000+

Factors Affecting Cost:

• Number of patient records
• Data complexity
• Old system compatibility
• Custom fields and templates

DIY Option: Some vendors allow self-migration (time-consuming but free)

Integration Costs

Common Integrations:

• Lab systems: $50-150/month
• Imaging systems: $75-200/month
• Billing clearinghouses: $30-100/month
• Telehealth platforms: $30-100/month
• Patient engagement: $50-150/month
• Accounting software: $20-75/month

Total Integration Costs: $200-800/month for full integration suite

Questions to Ask:

• Which integrations are included?
• Which cost extra?
• Are there setup fees for integrations?
• Can I add/remove integrations easily?

Support and Maintenance

Support Tiers:

• Basic (email only): Usually included
• Standard (email + phone): $0-50/month
• Priority (faster response): $50-150/month
• Premium (dedicated rep): $150-500/month

What's Covered:

• Technical support
• Bug fixes
• Security updates
• Feature updates

What Costs Extra:

• Custom development
• Workflow consulting
• Advanced training
• On-site support

Budget: $0-150/month depending on needs

Storage and Usage Fees

What Triggers Fees:

• Document storage over limit
• Number of patient records
• Data backup and archiving
• API calls over limit

Typical Costs:

• Storage: $10-50/month per 100GB
• Overage fees: $0.10-0.50 per GB
• API calls: $0.01-0.10 per 1,000 calls

Questions to Ask:

• What's the storage limit?
• What happens when I exceed it?
• Are there patient record limits?
• Are backups included?

Contract and Cancellation Fees

Common Fees:

• Early termination: $500-5,000
• Data export: $500-2,000
• Contract renewal: $200-1,000
• Downgrade fees: $100-500

Questions to Ask:

• What's the contract length?
• Can I cancel anytime?
• What's the cancellation fee?
• How do I get my data if I leave?
• Is there a notice period?

Red Flags:

• Multi-year contracts with no escape clause
• High early termination fees
• Difficulty exporting data
• Automatic renewal without notice

Feature Add-On Costs

E-Prescribing

Typical Cost: $20-50/month per provider

What's Included:

• Electronic prescription sending
• Medication history
• Formulary checking
• Prior authorization

Watch Out For:

• EPCS (controlled substances) may cost extra ($10-30/month)
• State-specific requirements
• DEA registration fees (separate)

Billing and Claims

Typical Cost: $50-150/month or per-claim fees

What's Included:

• Claims submission
• Payment posting
• Denial management
• Patient statements

Watch Out For:

• Per-claim fees on top of monthly fee
• Clearinghouse fees ($30-100/month)
• ERA/EFT fees ($20-50/month)
• Statement printing/mailing ($1-3 per statement)

Telehealth

Typical Cost: $30-100/month per provider

What's Included:

• Video conferencing
• Screen sharing
• Session recording
• Waiting room

Watch Out For:

• Per-minute charges
• Participant limits
• Storage fees for recordings
• HIPAA compliance features

Patient Portal

Typical Cost: $20-60/month

What's Included:

• Secure messaging
• Appointment requests
• Document access
• Bill payment

Watch Out For:

• Per-patient fees
• Transaction fees on payments (2-3%)
• SMS notification fees ($0.01-0.05 per message)
• Custom branding fees

Reporting and Analytics

Typical Cost: $30-100/month

What's Included:

• Standard reports
• Custom report builder
• Data export
• Dashboards

Watch Out For:

• Advanced analytics extra
• Custom report development fees
• Data warehouse access
• API access for external tools

Real-World Cost Comparisons

Scenario 1: Solo Therapist

SimplePractice:

• Base: $99/month
• Telehealth: Included
• Billing: Included
• Total: $99/month

TherapyNotes:

• Base: $49/month
• Telehealth: $30/month
• Total: $79/month

ClinikEHR:

• All features: Free (Starter) or $99/month (Professional)
• Total: $0-99/month

Winner: ClinikEHR for budget, SimplePractice for features

Scenario 2: Small Primary Care (3 Providers)

Athenahealth:

• 6% of collections
• Collecting $50,000/month
• Total: $3,000/month ($36,000/year)

DrChrono:

• $199/month × 3 providers = $597/month
• E-prescribing: $30/month × 3 = $90/month
• Billing: $150/month
• Total: $837/month ($10,044/year)

ClinikEHR:

• Professional: $99/month (unlimited providers)
• Total: $99/month ($1,188/year)

Winner: ClinikEHR saves $8,856-34,812/year

Scenario 3: Group Mental Health (10 Providers)

SimplePractice:

• $99/month × 10 providers = $990/month
• Total: $990/month ($11,880/year)

TheraNest:

• $39/month × 10 providers = $390/month
• Total: $390/month ($4,680/year)

ClinikEHR:

• Professional: $99/month (unlimited providers)
• Total: $99/month ($1,188/year)

Winner: ClinikEHR saves $3,492-10,692/year

How to Budget Accurately

Step 1: Calculate Base Cost

Questions to Answer:

• What's the monthly subscription?
• How many providers?
• What tier do I need?
• Is there a discount for annual payment?

Formula:

Base Cost = Monthly Fee × Number of Providers × 12 months

Step 2: Add Essential Features

Must-Have Features:

• E-prescribing (if applicable)
• Billing and claims
• Patient portal
• Telehealth (if offering)

Formula:

Feature Costs = Sum of all required add-ons × 12 months

Step 3: Include One-Time Costs

Initial Expenses:

• Setup and implementation
• Training
• Data migration
• Hardware (if needed)

Formula:

One-Time Costs = Setup + Training + Migration + Hardware

Step 4: Factor in Hidden Costs

Ongoing Expenses:

• Integrations
• Premium support
• Storage overages
• Transaction fees

Formula:

Hidden Costs = Monthly extras × 12 months

Step 5: Calculate Total Cost of Ownership

Complete Formula:

Year 1 Total = Base Cost + Feature Costs + One-Time Costs + Hidden Costs

Year 2+ Total = Base Cost + Feature Costs + Hidden Costs

Example:

Year 1:
Base: $199/month × 12 = $2,388
Features: $150/month × 12 = $1,800
One-time: $1,500
Hidden: $50/month × 12 = $600
Total Year 1: $6,288

Year 2+:
Base: $2,388
Features: $1,800
Hidden: $600
Total Year 2+: $4,788/year

Step 6: Compare to Revenue

Healthy Benchmark: EHR costs should be 1-3% of practice revenue

Example:

Practice Revenue: $200,000/year
EHR Budget: $2,000-6,000/year (1-3%)

If EHR costs $8,000/year = 4% (too high)
If EHR costs $1,000/year = 0.5% (good value)

Questions to Ask Before Buying

Pricing Questions

1. What's included in the base price?
2. What features cost extra?
3. Are there per-claim or per-patient fees?
4. What are the setup and training costs?
5. Is there a contract? How long?
6. What's the cancellation policy?
7. Are there price increases? How often?
8. Is there a discount for annual payment?
9. What happens if I exceed usage limits?
10. Are there any other fees I should know about?

Feature Questions

1. Which features are included vs. add-ons?
2. Can I add features later?
3. Can I remove features to reduce cost?
4. Are integrations included?
5. Is support included? What level?
6. Are updates and upgrades included?
7. Is data storage unlimited?
8. Are there user limits?

Contract Questions

1. What's the minimum contract length?
2. Can I cancel anytime?
3. What's the notice period?
4. Are there early termination fees?
5. Does it auto-renew?
6. Can I downgrade my plan?
7. What happens to my data if I cancel?
8. Is there a data export fee?

Red Flags to Watch For

Pricing Red Flags

• Unwilling to provide clear pricing
• "Call for pricing" with no transparency
• Hidden fees buried in fine print
• Per-claim fees not disclosed upfront
• Automatic price increases without notice
• Fees for basic features
• High early termination penalties

Contract Red Flags

• Multi-year contracts required
• No trial period
• Difficult cancellation process
• Data held hostage after cancellation
• Automatic renewal without opt-out
• Penalties for downgrading
• Vague terms and conditions

Vendor Red Flags

• Pushy sales tactics
• Unwilling to answer questions
• No customer references
• Poor online reviews
• Frequent complaints about billing
• Lack of transparency
• No clear roadmap or updates

Money-Saving Tips

1. Start with Free or Low-Cost Options

Free EHRs:

• ClinikEHR Starter (Free forever)
• OpenEMR (Open source, self-hosted)
• FreeMED (Open source)

Low-Cost Options:

• ClinikEHR Professional ($99/month, unlimited)
• TheraNest ($39/month per provider)
• Practice Fusion ($149/month)

2. Negotiate

What's Negotiable:

• Setup fees (often waived)
• Training costs (ask for free)
• Contract length (shorter is better)
• Annual payment discount (10-20%)
• Multi-provider discount
• Non-profit discount

How to Negotiate:

• Get quotes from 3-5 vendors
• Mention competitor pricing
• Ask about promotions
• Request waived setup fees
• Negotiate annual payment discount

3. Avoid Unnecessary Add-Ons

Start Minimal:

• Begin with core features only
• Add features as needed
• Don't pay for unused features
• Review usage quarterly

Common Unnecessary Add-Ons:

• Advanced analytics (if you don't use data)
• Premium support (if basic is sufficient)
• Integrations you don't need
• Features for future "maybe" needs

4. Choose Flat-Rate Pricing

Benefits:

• Predictable budgeting
• No surprise fees
• Scales with practice growth
• Simpler accounting

Best For:

• Growing practices
• Multiple providers
• High claim volume
• Budget-conscious practices

5. Pay Annually

Typical Savings: 10-20% vs. monthly

Example:

Monthly: $99/month × 12 = $1,188/year
Annual: $999/year (16% savings)
Savings: $189/year

Considerations:

• Only if you're confident in the system
• After trial period
• If cash flow allows
• Check refund policy

Frequently Asked Questions

Pricing Models

Q: Which pricing model is best for solo practitioners? A: Flat-rate unlimited pricing offers the best value for solo practitioners. You get all features without per-claim fees or usage limits. ClinikEHR's $99/month (or free Starter plan) includes everything you need without hidden costs.

Q: When does percentage-of-collections pricing make sense? A: Only if you want full billing outsourcing and collect over $100,000/month. Below that, flat-rate pricing is almost always cheaper. Calculate carefully—6% of $50,000/month is $3,000/month ($36,000/year) vs. $99-300/month for flat-rate.

Q: Are per-claim fees ever a good deal? A: Rarely. Per-claim fees only make sense if you submit fewer than 20-30 claims per month. For most practices, flat-rate pricing is more economical and predictable.

Hidden Costs

Q: What are the most common hidden costs? A: Setup fees ($500-5,000), training ($200-2,000), data migration ($500-3,000), per-claim fees ($0.50-3.00), integration costs ($50-200/month), and feature add-ons ($100-300/month). Always ask for total cost including all fees.

Q: How can I avoid hidden fees? A: Ask for a complete cost breakdown in writing before signing. Request a sample invoice showing all charges. Read the contract carefully. Choose vendors with transparent, all-inclusive pricing like ClinikEHR.

Q: What should I budget for EHR costs? A: Plan for 1-3% of practice revenue. For a $200,000/year practice, budget $2,000-6,000/year for EHR. Include base cost, features, training, and hidden fees in your calculation.

Contracts and Commitments

Q: Should I sign a long-term contract? A: Avoid multi-year contracts when possible. Start with month-to-month or annual contracts. You need flexibility to switch if the system doesn't work. Never sign a 3-5 year contract without a trial period.

Q: What if I want to cancel? A: Check the cancellation policy before signing. Look for: notice period (30-90 days), early termination fees, data export process, and refund policy. Avoid vendors that make cancellation difficult.

Q: Can I get my data if I switch EHRs? A: You should be able to export your data in standard formats (CSV, PDF, CCD). Some vendors charge $500-2,000 for data export. ClinikEHR provides free data export anytime.

Feature Costs

Q: Which features should I pay extra for? A: Only pay for features you'll actually use. Essential features (scheduling, notes, billing) should be included. Consider paying extra for: e-prescribing (if you prescribe), telehealth (if you offer it), and integrations you need.

Q: Are "all-inclusive" plans really all-inclusive? A: Not always. Verify what's included: all features, unlimited users, unlimited claims, integrations, support level, and storage. ClinikEHR's plans are truly all-inclusive with no hidden fees.

Q: How much should e-prescribing cost? A: $20-50/month per provider is typical. EPCS (controlled substances) may cost extra ($10-30/month). Some EHRs include e-prescribing free. Factor this into total cost if you prescribe medications.

Budgeting

Q: What's a reasonable EHR budget for a solo practitioner? A: $0-200/month ($0-2,400/year) is reasonable. ClinikEHR offers a free plan for solo practitioners. Paid plans with all features range from $99-200/month. Avoid systems costing over $300/month unless you have specific needs.

Q: How much does EHR cost for a 5-provider practice? A: With per-provider pricing: $500-2,500/month ($6,000-30,000/year). With flat-rate pricing: $99-500/month ($1,188-6,000/year). Flat-rate saves $4,812-24,000/year for a 5-provider practice.

Q: Should I factor in staff time for implementation? A: Yes. Budget 20-40 hours of staff time for setup, training, and transition. At $25/hour, that's $500-1,000 in labor costs. Choose systems with easy setup and good training to minimize this cost.

The Bottom Line

EHR pricing is complex, but it doesn't have to be confusing. The key is understanding the total cost of ownership, not just the advertised price.

Key Takeaways:

1. True cost is 40-60% higher than advertised due to add-ons and hidden fees
2. Flat-rate pricing offers best value for most practices
3. Per-claim fees penalize growth and create unpredictable costs
4. Percentage-of-collections is expensive unless you need full RCM outsourcing
5. Always ask for total cost in writing before signing

Budget Formula:

Total Year 1 Cost = Base + Features + Setup + Training + Migration + Hidden Fees
Total Year 2+ Cost = Base + Features + Hidden Fees

Healthy Range: 1-3% of practice revenue

Best Value: ClinikEHR offers transparent flat-rate pricing with all features included, no per-claim fees, and no hidden costs. Free plan available for solo practitioners.

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Related Reading on ClinikEHR

• EHR comparison: SimplePractice vs Alternatives | Best EHR for Solo Practice | Best EHR for Small Practices
• Budget options: Top 5 Free EHR for Private Practice | Low-Cost EHR for Mental Health Clinics
• Specialty guides: Best EHR for Mental Health | Best EHR for Psychiatrists | Best EHR for Counseling
• Switching guides: How to Switch EHR Without Losing Data | Private Practice EHR Buyers Guide
• Features: Top EHR Features to Look For | Best EHR for Multiple Providers

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Last updated: January 2026. Pricing and features subject to change. Always verify current pricing with vendors before purchasing.