Key points
- A three-year total adds setup, migration, training time, payment processing and contract terms to the subscription.
- In a study of 26 Texas primary care practices, an average five-physician practice spent an estimated $162,000 to implement an electronic record, with $85,500 of maintenance in the first year.1
- The same study counted 134 hours of preparation per physician for clinicians and staff before go-live.1
- ONC's contract guide notes that interfaces may attract additional fees and that a short non-renewal notice period can be used to raise fees.2
- wai publishes its prices, and Checkout carries no wai subscription or setup fee.34
Summary
Clinic management software costs its subscription plus setup, migration, training time, payment processing and any usage or interface fees. Add these up over three years, per clinician and per location, and get every line in writing before you sign.
You sign knowing the three-year number, with the subscription, the payment fees and your team's learning hours all on one page. The worksheet below gets you there in an afternoon.
See it in your clinicThirty minutes on your own patients and doctors.
Request a demoSee the published price of every wai plan applied to your own clinicians and locations, with the three-year total worked out live.
| Cost line | What drives it | Question to ask in writing |
|---|---|---|
| Setup and onboarding | Configuration, templates, connections to phones and calendars | Is setup a one-off fee, included, or waived on an annual term |
| Per-seat licences | Number of clinicians, and sometimes admin staff | Which roles need a paid seat, and is there a minimum |
| Per-location fees | Number of sites | What one location includes, and what a second adds |
| Usage allowances | Notes, messages or actions per month | What happens beyond the allowance, and who agrees it first |
| Payment processing | Card revenue taken through the system | Does the software add a percentage on top of the processor's rate |
| Migration | Records, documents and appointments moved from the old system | Is migration priced, and who checks the imported data |
| Training time | Hours for clinicians and staff before go-live | How many hours per role, and is training included |
| Integrations | Labs, prescribing, insurers and other software | Are interfaces in the quoted price, including existing ones |
| Regulatory updates | Changes in law and reporting rules | Are updates included in the base fee |
| Renewal and exit | Price rises, notice periods, export and transition help | What is the renewal uplift, and what does an export cost |
Ten lines make up the cost
Every clinic system is paid for across the same cost lines, itemised or folded into one fee. The table below gives each line, its driver and the question to ask in writing. Setup and migration are paid once, and seats and payment fees repeat monthly.
What implementation cost in a measured study
A 2011 study of 26 primary care practices in a north Texas physician network gives the most detailed public costing. For an average five-physician practice, implementing an electronic health record cost an estimated $162,000, with $85,500 in maintenance during the first year.1 The network's implementation team and the practice team needed 611 hours on average to prepare and go live.1
Physicians, other clinical staff and non-clinical staff needed 134 hours per physician on average to prepare for using the record in clinical encounters.1 Hosted software needs far less hardware than in 2011, so the time line is the one to price. Cost training hours at your loaded hourly rate and add them to the total.
Costs written into the contract
The Office of the National Coordinator for Health IT published a buyer's guide to electronic record contracts in 2016. Interfaces to other software, including existing ones, may need customisation and additional fees, so get them into the quoted price.2 Ask whether regulatory updates are included in the base fee.2
A non-renewal notice given too close to expiry for the clinic to move can be used to raise fees.2 The guide advises agreeing transition assistance at the start, including a stated period of access after the contract ends.2 The exit side is in the clinic software switching checklist.
Payments are a cost line of their own
Ask whether any percentage or fixed fee sits on top of the card processor's rate, and whose merchant account the money lands in. Multiply expected card revenue by every fee on the payment path over three years, and put that figure on its own line.
The three-year worksheet
Year one adds setup, migration, training hours at your hourly cost, twelve months of seats and locations, and payment fees on expected card revenue. Years two and three add subscriptions with any renewal uplift, payment fees, usage beyond the allowance and paid add-ons.
Divide the total by expected appointments. Cost per appointment puts per-seat and per-location pricing on the same scale, and sits directly against the hours and bookings the system returns.
How wai prices
wai publishes its prices on the pricing page, for the reasons in why we publish our prices. Clinician plans are priced per clinician, billed monthly and cancelled in settings, and a seven-day trial for one clinician has limited use.3 Notes and records can be exported.3
wai Checkout has no wai subscription or setup fee, and card payments run through the clinic's own Stripe account at Stripe's published rate, with the clinic as merchant of record.34 Admin is priced per location with a monthly credit allowance, and anything beyond it is agreed before it is billed.3 An annual agreement includes Admin setup and holds the rate for the full term.3 Published entry prices across the category are in the private practice EHR price index.
Where to start
Send the table below for your number of clinicians and locations, and ask for every line in writing over three years.
Fill the worksheet, set cost per appointment against the hours and bookings returned, and sign once the three-year number fits on one page for your partners.
Bring your clinician count, your locations and last year's card revenue, and see the three-year worksheet filled with our published prices.
Frequently asked questions
How much does clinic management software cost?
It depends on clinicians, locations, card revenue and contract terms, so work from a written three-year total. Published entry prices are in the private practice EHR price index.
Which costs sit outside the subscription?
Interfaces, regulatory updates, usage beyond allowances, payment fees above the processor's rate, and renewal terms. ONC's contract guide notes that even existing interfaces may attract additional fees.2
How much staff time does a new system take?
Plan for it. In a study of Texas primary care practices, clinicians and staff needed 134 hours per physician on average to prepare for an electronic record.1 Hosted software may need fewer, and the hours still go in the total.
Is per-seat or per-location pricing cheaper?
Per-seat pricing suits clinics with few clinicians, and per-location pricing suits busy sites with many. Divide each three-year total by expected appointments to see which fits.
Does wai charge a fee on card payments?
Checkout carries no wai subscription or setup fee. Card payments run through the clinic's own Stripe account at Stripe's published rate, and the clinic is the merchant of record.4
Sources
- 1Health Affairs, Fleming et al., 2011The financial and nonfinancial costs of implementing electronic health records in primary care practicesRead 14 October 2026Read source
- 2Office of the National Coordinator for Health Information Technology, 2016EHR Contracts Untangled, selecting wisely, negotiating terms and understanding the fine printRead 14 October 2026Read source
- 3wai, 2026AI scribe and clinic software pricingRead 14 October 2026Read source
- 4wai, 2026wai CheckoutRead 14 October 2026Read source
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