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WebPT EMR + Billing: Best Practices

There are a lot of things to remember when you’re beginning to use WebPT EMR + Billing. In this article, you’ll find some tips that will help you get the most out of the software.

Required Patient Information

As you add patients in the WebPT EMR, remember:

  • Referring Physician address fields longer than 32 characters are truncated
  • Only the Primary patient address and phone number are transmitted
  • If an Authorization is required, you must indicate this on the patient’s case.
  • If the KX modifier is needed, you’ll need to select the KX radio button from the Apply Modifier section of the patient’s case. If this is not done, it will need to be manually added using the Charge Review page in WebPT Billing.
  • Emergency Contact information does not import from the WebPT EMR. Use the Emergency Contact section in WebPT Billing to add that information. Tip: Click Edit Patient in the bottom right to update these fields.
  • Ensure that all therapists assigned to patient cases are current (active providers at your organization).  Be sure to use the User Manager Search before adding a new provider.

Quick Add Patient

The Quick Add functionality allows you to quickly create patients and get them scheduled without a complete patient profile. However, therapists won't be able to finalize notes for patients with incomplete profiles until their patient information is completed. This ensures that only completed patient records flow into Billing, preventing Billing Exceptions and billing delays. We only recommend enabling Quick Add if your practice has strong patient information collection workflows, otherwise, your therapists may be prevented from finalizing notes in a timely manner.

For more information, please see: Required Patient Information.


When adding authorizations to the patient’s case in the WebPT EMR, be sure to include an authorization number or add 0000 as a placeholder. Otherwise, any visits requiring this auth will be held on Delayed Claims.

Once you add an authorization and save the patient, the authorization automatically flows into WebPT Billing, as long as the date you add the authorization is within the authorization effective dates. 

For more information, please see: Authorizations: WebPT EMR + Billing


When finalizing an addendum (SOAP 1.0 and SOAP 2.0) in the WebPT EMR, we recommend selecting Finalize for updates that don’t impact the claim (i.e. updates to the pain scale) and selecting Finalize & Rebill for updates that do impact the claim (i.e. units being added or removed). Once you finalize the addendum, the information will flow into WebPT Billing and automatically update. Billers should work the Charge Updates report daily to confirm that any addended dates of service are billed properly and if a corrected claim is required.

For more information, please see the Addendum Workflow.

Adding and Editing Providers

Users should never have more than one set of credentials for the WebPT EMR or WebPT Billing, as each user can be granted access to multiple clinics and companies. If you need to edit a user’s login, name, password, or permissions, click here to learn how.

It’s crucial that providers are not duplicated in the WebPT EMR. Duplicate providers create issues with your billing database and can lead to delays in submitting claims. Before creating a new provider in the WebPT EMR, confirm that the provider is not already in the system (under another location, a previous name, or login). 

  • If you locate the provider, update the provider's profile to reflect the correct information.
  • If you have confirmed that the provider is not in the WebPT EMR:
    • Add the provider in the WebPT EMR.
    • The provider will be automatically created in WebPT Billing and appears on the Incomplete Constants report. You'll need to update the provider code, click here for instructions.

Patient Payments/Copays

All patient payments, including copays, supplies, and miscellaneous fees, should be entered into the WebPT EMR and allowed to flow into WebPT Billing. This is true for both insurance and Self Pay cases. While the payments will be entered into the EMR directly, some charges may need to be manually added to WebPT Billing.

For more information, please see: Post Interest, Medical Record Fees, Supply Payments, and Insurance Overpayments

Custom Codes (WebPT EMR)

Use Custom Codes to bill for anything you’d like to charge for outside of the standard charge codes. This includes items like supplies, wellness programs, self-pay patients, or gym memberships. If you will be billing a patient directly, you can add the Self Pay insurance to the case in the WebPT EMR. You will be able to document and use Custom CPT codes to charge amounts that differ from the comparative CPT codes. 

For more information, please see: Custom Codes.

Add Charges (WebPT Billing)

To bill your patients for various non-CPT charges directly in WebPT Billing, such as a fee for a missed appointment, manually add the charges to a Self Pay case in WebPT Billing. The payments for these charges will need to be entered into the WebPT EMR and allowed to flow into WebPT Billing.

For more information, please see: Add Charges

NORCM: Prevent Charges from Flowing into WebPT Billing (SOAP 1.0)

Prevent specific Dates of Service or charges from flowing into Billing. 

Important: This only works for SOAP 1.0 documentation. Click here to learn how.

Do Not Bill: Prevent Notes/Charges from Flowing into WebPT Billing (SOAP 2.0)

Located in the Charge Summary, the Do Not Bill checkbox allows you to finalize a note without CPT codes attached. This will prevent notes from flowing into WebPT Billing. For more information, click here.

Medical Records & Fees

To bill your patients for various non-CPT charges, such as a fee for a missed appointment, manually add the charges to a Self Pay case in Billing. The payments for these charges will need to be entered into the WebPT EMR and allowed to flow into Billing.

For more information, please see: Add Charges.

DME (Durable Medical Equipment)

In order to successfully bill DME, or Durable Medical Equipment, for reimbursement, a specific Medicare DME payer must be set up correctly in Billing. If this payer was not created during onboarding, please email edi.help@webpt.com. Please include the Medicare DME PTAN and NPI used for billing in the request. 

To see the workflow for documenting DME, please see: DME Cases.

Changing Insurance Mid-Treatment

When a patient changes insurance mid-treatment, it is important that a new case is created so that information flows into Billing correctly.

For more information, please see: Changing Insurance Mid-Treatment (SOAP 1.0) or Change Insurance Mid-Treatment (SOAP 2.0)


Account Notes are a convenient way to communicate information about a patient. For more information, please see: Account Notes and Sticky Notes.


For common problems and solutions, please see Troubleshooting.

Updates, EDI, and Support 

  • There are designated email addresses for you to contact when updates or corrections need to be made on patient accounts or to your WebPT Billing account. The following is a list of updates and questions and where they should be sent. If you are unsure of where to send a specific inquiry, contact your Customer Service Rep and they will route it appropriately. For more information, please see: Updates, EDI, & Support.
  • For questions regarding WebPT Billing, system errors, training, or enhancements requests, please send an email to WebPTBillingSupport@WebPT.com.
  • For questions regarding the WebPT EMR, please email support@webpt.com.
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