Software for Physical Therapy Practices: The Complete Stack (2026)

What a physical therapy practice needs from its software

A PT clinic has more rules attached to each visit than most small practices. Patients come in two or three times a week for weeks at a time, most visits are billed in 15-minute timed units, and Medicare adds its own paperwork on top. The software has to track all of that without slowing therapists down. These are the requirements that matter most for an outpatient clinic with 1 to 10 therapists.

Plan of care certification. Medicare pays for outpatient therapy only under a plan of care that a physician or nonphysician practitioner (NPP) certifies. CMS's Benefit Policy Manual says the initial plan should be certified as soon as possible, which it defines as within 30 days of the first treatment, including the evaluation. A verbal order must be followed by a signature within 14 days. A certification covers the length of the plan or 90 calendar days, whichever is less, and the plan must be recertified at least every 90 days or when it changes significantly. Your EMR should send the plan to the referring provider, track whether it came back signed, and warn you before a certification runs out.

Progress reports. The same manual requires a progress report at least once every 10 treatment days. This is a separate clock from recertification. Good rehab EMRs count treatment days for each patient and flag the visit when a report is due.

The 8-minute rule for timed codes. CMS's Claims Processing Manual says you bill one unit of a timed code for 8 to 22 minutes, two units for 23 to 37 minutes, three for 38 to 52, and so on. Minutes for several timed codes on the same day are added together before you work out the units. Software should calculate units from the minutes the therapist records and stop a claim that bills more units than the minutes support. When a PT assistant delivers part of a service, CMS requires the CQ modifier on the units the assistant furnished, and the units have to be split correctly between the therapist and the assistant.

The KX modifier threshold. Medicare no longer caps therapy, but it keeps a threshold. For 2026, CMS lists $2,480 for PT and speech-language pathology combined. Claims above that amount must carry the KX modifier to confirm the care is medically necessary, and CMS denies claims over the threshold that lack it. Claims above $3,000 can be picked for targeted medical review. Your system should track each Medicare patient's running total for the year, including visits at other clinics where you know about them, and prompt for KX at the right point.

Outcome measures and MIPS. Physical therapists are MIPS eligible clinicians. For 2026, the QPP site says a clinician or group must report only if they bill more than $90,000 in Medicare Part B covered professional services, see more than 200 Part B patients, and provide more than 200 covered services. Many small clinics fall below one of these, but a busy Medicare clinic may not. Look for standardized functional outcome tests built into the note and automated MIPS tracking. WebPT lists 200+ standardized tests and MIPS tracking through its own QCDR.

Direct access. APTA reports that as of July 1, 2025, all 50 states, DC and the US Virgin Islands allow some form of direct access to physical therapy, though some states still attach conditions to treatment without a referral. Your intake should record whether the patient has a referral and which state rules apply. Medicare patients still need a certified plan of care whatever your state allows.

Home exercise programs. HEP is part of almost every PT episode. It is easiest when the exercise library, the patient app and the note live in the same system, so the program is documented automatically.

High-volume scheduling and no-shows. A clinic booking patients three times a week for six weeks needs recurring appointments tied to the plan of care, a waitlist to fill cancellations, and text reminders. Each empty slot is lost revenue that cannot be rebooked.

Billing, denials and authorizations. Commercial payers often limit visits or require authorization. The software should track authorized visits and expiry dates, check eligibility before the first visit, and scrub claims for coding errors before they go out.

All-in-one or separate tools?

For most PT clinics, one rehab-specific system is enough. WebPT, Prompt Health and SPRY combine documentation, scheduling and insurance billing, and each has tools for eligibility, claim scrubbing and denials. Prompt includes reminders, digital intake and HEP in its per-provider plan. SPRY is ONC certified and offers a separate billing service. WebPT includes a 5,500+ exercise HEP and outcome measures. These suit clinics where Medicare and commercial insurance make up most of the revenue.

PtEverywhere and HENO are also PT-only systems, with published prices. PtEverywhere leans toward cash-pay and hybrid clinics that sell packages and memberships, and adds insurance billing as an add-on. HENO includes billing software and a clearinghouse on every plan, with HEP and texting on higher tiers.

Jane is the common choice for multidisciplinary clinics with PT, chiropractic and massage under one roof. Its booking and patient app are strong, but it is not built around plans of care, the 8-minute rule or MIPS, so an insurance-heavy PT clinic should test those workflows carefully.

Raintree Systems is built for groups from about five clinics up. A clinic planning several locations may look at it; a single small clinic will usually find it more than it needs.

Separate tools make sense in four cases:

• Outsourced billing. If you would rather hand off billing, Athelas runs managed billing with a PT focus. CollaborateMD suits clinics that keep their EMR but want a separate billing system.
• AI scribe. WebPT, Prompt, SPRY's Plus plan and PtEverywhere include AI documentation. If yours does not, a standalone scribe such as Freed or Heidi can draft notes for you to paste in. Check that it captures treatment minutes, which drive your units.
• Phones and texting. Front desks in busy clinics miss calls. Lydoh handles missed-call texts and after-hours answering, PatientCalls offers live answering, and Spruce or Weave combine phones and texting.
• HIPAA compliance. No EMR runs your risk analysis, policies and staff training for you. A program such as Accountable or Compliancy Group covers that.

What physical therapy software costs

Prices below are list prices as of November 2026, taken from the vendors' pricing pages. Prompt Health, Raintree and SPRY do not publish prices, so you will need quotes to compare them.

Core system, per month:

• WebPT: $79 to $249 per provider. WebPT does not say what each tier includes, so treat $79 as the floor.
• PtEverywhere Standard: $149 including one therapist, then $75 per therapist for seats 2 to 5, $60 for seats 6 to 10. Insurance billing (RCM) is $39 per therapist more.
• Jane Practice: $79 including one full-time practitioner, then $35 per extra full-time practitioner. Insurance billing adds $20 a month plus $5 per extra practitioner.
• HENO Growth: $149 per provider on a one-year contract, with billing and clearinghouse included.

Common add-ons: Accountable Basic HIPAA is $169 a month billed annually ($2,028 a year), covering 15 employees. Lydoh After Hours is $99 a month. Freed Core is $59 to $79 per clinician a month depending on billing term.

Typical totals for the core system plus a compliance program:

• Solo therapist: about $250 to $420 a month, or $3,000 to $5,000 a year. Jane with insurance billing is $99 a month; PtEverywhere Standard is $149; WebPT starts at $79.
• 3 therapists: about $350 to $920 a month, or $4,200 to $11,000 a year. Jane with insurance billing comes to $179; PtEverywhere with RCM to $416; HENO to $447; WebPT to $237 to $747.
• 10 therapists: about $650 to $2,700 a month, or $7,800 to $32,000 a year. Jane with insurance billing is $459; PtEverywhere with RCM is $1,139; HENO is $1,490; WebPT is $790 to $2,490. Accountable adds $9 per employee beyond 15.

Outsourced billing is usually priced as a percentage of collections, which can exceed the software cost. Try your own numbers in the software cost calculator.

Compliance checklist for physical therapy practices

• Sign a business associate agreement with every vendor that stores or sends patient data: EMR, billing service, HEP app, texting, phones, scribe and fax. HHS lists what the contract must contain, including safeguards, breach reporting and return or destruction of data at the end.
• Run and document a HIPAA risk analysis. HHS calls it the first step in Security Rule compliance and expects it to be updated as your systems change. Include tablets used for intake and therapists' phones used for HEP.
• Get plans of care certified on time: within 30 days of the first treatment, signature within 14 days of a verbal order, and recertification at least every 90 days.
• Write progress reports at least once every 10 treatment days for Medicare patients.
• Bill timed codes by the 8-minute rule, and add the CQ modifier for units furnished in whole or in part by a PT assistant.
• Track the 2026 KX threshold of $2,480 and add KX only when documentation supports medical necessity. Expect review risk above $3,000.
• Check your MIPS status each year on the QPP site against the low-volume threshold.
• Confirm your state's direct access rules for treatment without a referral, and record referral status at intake.

Questions to ask in a demo

• How does the system track plan of care certification and warn me before the 90-day recertification?
• Does it count treatment days and flag when a Medicare progress report is due?
• Does it calculate units from recorded minutes under the 8-minute rule, including mixed timed codes?
• How does it handle CQ modifiers when an assistant treats part of a visit?
• Does it track each patient's running Medicare total against the KX threshold?
• Which functional outcome measures are built in, and do you submit MIPS data for us?
• How are commercial authorizations and visit limits tracked, and what happens when a patient runs out?
• Is the home exercise program included, and can patients use it on their phones?
• Can I book recurring visits from the plan of care, and is there a waitlist that texts patients to fill cancellations?
• Is the AI scribe included, and does it capture treatment minutes?
• What is the denial rate for your PT customers, and is the clearinghouse included in the price?
• Will you sign a BAA, and what does it cost to export all my data if I leave?