Physical Therapy Billing Software
Built for Home Health PT Contract Agencies.
Bill home health companies per PT visit. Run 1099 PT contractor payroll from the same data. Track certification periods and 30-day re-evals automatically. The physical therapy billing software built for the home health PT contract model — not for outpatient clinics chasing insurance claims.
30-day free trial · No credit card · Setup in under 10 minutes
I'm a home health PT, and I ran a contract therapy agency placing PTs with home health companies. Every billing tool I tried was built for clinic insurance billing or full Medicare EMRs — not for the per-visit, multi-agency, 1099-PT-payroll workflow I actually ran. So I built one that fits the model. My own agency runs on it.
Two Very Different Kinds of "Physical Therapy Billing Software"
Search "physical therapy billing software" and you'll get two very different categories of tools mixed together — and the right one for you depends entirely on which side you operate on.
1. Outpatient PT Clinic Insurance Billing
Built for PT clinics that bill Medicare and commercial insurers directly. Features: CPT coding, claim scrubbing, clearinghouse submission, ERA/EOB posting, prior authorization tracking, MIPS reporting. Examples: WebPT, Therabill, Kareo. If you run a clinic, this is your category — HomeHealthSync is not it, and we'll tell you that upfront.
2. Home Health PT Contract Therapy Agency Billing
Built for therapy vendors and agencies that contract 1099 PTs and place them with home health companies. The agency invoices each home health company per visit at a contracted rate, then pays each PT from the same visit data. Features: per-agency PT rate matrices, multi-agency invoicing, integrated 1099 PT contractor payroll, HIPAA-compliant invoice delivery, 30-day re-eval tracking. This is what HomeHealthSync is built for.
Mixing these up is expensive. A PT contract agency paying for WebPT ends up with deep CPT/payer features they'll never use and no per-agency rate matrix or contractor payroll — the two things they actually need most.
The PT Contract Therapy Agency Workflow
If you run an agency where you contract PTs and place them with home health companies, your week looks like this:
- Your PTs see patients in the home health agency's patients' homes
- Each PT logs the visit — date, patient, visit type (PT eval, PT visit, PT re-eval, PT discharge), agency
- You invoice the home health agency for each PT visit at that agency's contracted rate
- You pay each PT their per-visit cut — often a different rate per visit type
- You do this across multiple home health agencies and multiple PTs simultaneously
- You track certification periods and 30-day re-evals to stay compliant for every PT, every patient
- Year-end: 1099-NECs for every PT paid $600+
None of that is insurance billing. None of it needs a clinic EMR. What it needs is a tool built around exactly that workflow.
Why Generic PT Software Doesn't Fit
What Physical Therapy Billing Software Actually Needs to Do (for a Contract Agency)
PT Payment Processing for Contract Agencies
For a contract therapy agency, "PT payment processing" runs in two directions: getting paid by the home health agencies you invoice, and paying your 1099 PT contractors. Both run through HomeHealthSync off the same submitted visit data.
On the inbound side, your invoices to home health agencies deliver through a HIPAA-compliant secure portal so agencies can pay you on their billing cycle. On the outbound side — the part most generic billing tools miss entirely — PT payment processing software for a contract agency needs to:
- Calculate each PT's pay automatically from the same visits used to invoice the home health agency (no parallel payroll sheet, no reconciliation)
- Apply each PT's individual per-visit-type rates (a PT eval pays differently than a regular PT visit or a discharge)
- Push payment directly to the PT's bank account via Stripe ACH — no check writing, no logging into a separate bank portal
- Log every payment automatically against year-to-date totals so 1099-NEC reporting in January is a one-click report, not a reconstruction project
That last point — automatic 1099-NEC tracking — is what most agencies underestimate until their first January. PT payment processing built for the contract therapy model handles it as part of the same workflow that invoiced the visit in the first place, not as a separate year-end scramble.
HomeHealthSync vs the Common Alternatives — For a PT Contract Agency
What It Costs
30-day free trial, no credit card required. Flat pricing — no per-user fees that scale with your PT roster.
Want to see this running for your PT agency?
“The invoices are automated so that saves me hours of work between 6 agencies we work with. It also auto-calculates certification periods and 30-day re-evals for therapists — a huge help for staying compliant. Also very mobile friendly!”
“Our admin staff loves it and reports it’s much better than the Excel system we had before. I like it a lot too. Of course there’s a small learning curve, but overall I’m happy with the purchase!”
Who This Is — and Isn't — For
HomeHealthSync is the right fit if you:
- Run a therapy agency that contracts 1099 PTs (alone or alongside OTs/STs)
- Place those PTs into home visits with home health companies
- Bill those home health companies per visit at contracted rates
- Pay PT contractors per visit, not by salary
- Need HIPAA-compliant invoice delivery + 1099-NEC tracking
HomeHealthSync is NOT the right fit if you:
- Run an outpatient PT clinic billing Medicare and commercial insurers (use WebPT)
- Need a clinical EMR with CPT coding, treatment notes, MIPS reporting
- Are a solo PT in private practice billing insurance directly
- Operate a Medicare-certified home health agency needing OASIS / PDGM (use WellSky)
Built for the PT Contract Therapy Model
Not adapted from clinic software. Not stripped down from enterprise EMR. Designed from scratch for agencies placing 1099 PTs with home health companies.
Frequently Asked Questions
What is the best physical therapy billing software for a home health PT contract agency?
HomeHealthSync is purpose-built for the model — per-agency PT visit rates, automated multi-agency invoicing, HIPAA-compliant delivery, integrated 1099 PT payroll, and direct Stripe payments. WebPT and Therabill are built for outpatient PT clinics billing insurance — a different workflow.
How is PT contract billing software different from WebPT or Therabill?
WebPT/Therabill submit CPT-coded claims to insurers — what an outpatient clinic does. PT contract agencies invoice the home health companies that contract their therapists, per visit at a contracted rate, and pay 1099 PTs from the same visit data. Different model, different software category.
Does HomeHealthSync handle PT certification periods and 30-day re-evals?
Yes — auto-calculated and flagged before the window closes. It's one of the most-cited features by admins juggling multiple agencies.
What features does PT billing software need for a contract agency?
Visit logging from the field, per-agency per-visit-type rate matrix, automated multi-agency invoicing, HIPAA-compliant delivery, integrated 1099 PT payroll, direct contractor payments, and re-eval tracking. Most general billing tools and insurance-billing EMRs miss several of these.
Can I use HomeHealthSync if I run an outpatient PT clinic billing insurance?
No — and we'll tell you that upfront. No CPT coding, no claim submission. For clinic insurance billing, WebPT or a comparable PT clinic EMR is the right tool. HomeHealthSync is specifically for the PT contract therapy agency model.
How much does PT contract therapy billing software cost?
$60/month for up to 8 active therapists or $149/month for unlimited. Both plans include visit tracking, multi-agency billing, HIPAA-compliant delivery, integrated 1099 contractor payroll, direct Stripe payments, and 1099-NEC tracking. 30-day free trial, no credit card required.
Ready to see it for your PT agency?