Quick Start: Billing


Billing for the first time can be intimidating, but with one-click electronic claim submission, simple CMS-1500 and superbill generation, easy-to-use reporting, integrated credit card processing, and more, TherapyNotes makes billing a breeze.

After you have scheduled an appointment and completed the corresponding note, your To-Do list will automatically create a reminder to submit the electronic claim, generate a CMS-1500 form, or mark that the claim was submitted outside of TherapyNotes, depending on your practice's default billing method or the billing method your set up for the specific payer. Simply enter any payment received from your client, let TherapyNotes help you generate and submit your claim, and enter the payment you receive from insurance.

This article is designed to help you set up your TherapyNotes account to be able to simply and efficiently bill for the services you provide. Be sure that you have configured the settings outlined in Quick Start: Set Up Your TherapyNotes Account before beginning this tutorial.

Role Required: Practice Biller or Practice Administrator

Follow the steps below to set up billing in TherapyNotes or click on any of the links below to jump to that section of the article.

Part 1: Practice Billing Settings

Click the User Icon > Settings > Practice Billing

Select the Enable Billing Features checkbox to display configurable billing settings for TherapyNotes.

Enable TherapyNotes EDI

Select the Enable TherapyNotes EDI checkbox to submit claims electronically within TherapyNotes.

EDI (electronic data interchange) allows TherapyNotes to submit your claims electronically to payers that you have added in TherapyNotes. Electronic claims in TherapyNotes pass through Change Healthcare, our clearinghouse partner who supports claim submission to over 2,000 payers nationwide.

Preferred Billing Methods

Select your default billing methods for in- and out-of-network payers. The billing method can also be adjusted per payer and per individual billing line item, if desired. Even if you are out-of-network with a payer, TherapyNotes can help you submit claims electronically on your client's behalf, saving your client from the hassle of submitting on their own and waiting for reimbursement.

Out-of-Network Payment Assignments

Select whether insurance payments should be assigned to the client or your practice on out-of-network claims.

(A) By default, payments should be assigned to the practice: This option assumes that the client is only responsible for paying their portion of the amount due (excluding the amount paid by the payer). This should be used when the practice submits the out-of-network claim and only charges the client the remainder of the balance not covered by insurance.

(B) By default, payments should be assigned to the patient: This option assumes that the client is responsible for paying the full amount due. This should be used when the client pays the entire balance upfront, the practice submits the out-of-network claim, and the payer reimburses the client directly.

Diagnosis Codes on Claims

Select whether to include only the primary diagnosis code or up to four diagnosis codes on electronic claims. Including multiple diagnoses per claim may be useful for payers who want to track information about co-occurring disorders, justifying diagnoses associated with medical conditions or substance use, and more.

Paper Claims

Configure your preferences for handling paper claims in TherapyNotes. When generating a CMS-1500 (formerly known as HCFA forms), TherapyNotes allows you to choose whether you want to print your data onto pre-printed red forms or you want to print the red form background along with your data. CMS-1500 forms can be purchased from a variety of places and may be required by some payers. Adjust your printer settings here to make sure the data you print lines up correctly with the pre-printed form.

Quick Tip: If a part of your data lines up perfectly at the top of the pre-printed CMS-1500 form, but the data at the bottom of the form does not, make sure that you are printing the document at 100% zoom without scaling.

Alternate Billing Address

If applicable, enter the alternate billing address for your practice here. An alternate billing address may be useful if you rent office space and want your billing correspondence sent to a home address or PO Box. 

When you are finished configuring your Practice Billing settings, click the Save Billing Settings button.

Part 2: Review Staff Roles for Billing

Click the User Icon > Settings > Staff User Accounts

Assign the role of Practice Biller to each staff user who needs to have access to practice-wide billing.

  • In the staff user's profile, click the Information tab
  • Click anywhere on the Roles box
  • Select the checkbox next to Practice Biller
  • Click the Save Changes button

Note: If a Clinician needs access to billing features such as entering rates, entering insurance information, and collecting copays, check the box next to Biller for Assigned Patients Only. This role does not let Clinicians submit any electronic claims, generate CMS-1500 forms, or generate superbills. It does enable Clinicians to add copays and insurance information for their clients.

Part 3: Adding Payers

TherapyNotes and Change Healthcare support claim submission to over 2,000 payers. To manage your insurance billing in TherapyNotes, add each of your payers.

Click Payers > Add a Payer

(A) Ins. Provider Name: Begin typing the insurance provider's name to see a list of exact or similar payer matches. Click on the payer in the list to automatically populate the Payer ID as well as information regarding the Clearinghouse EDI Enrollment Status for the payer.

(B) Network: Select the Network checkbox to indicate that you are in-network with the payer.

(C) Address, Phone Number, Fax Number: Generally, when submitting claims electronically, this information is not necessary. However, address information is required when submitting paper claims.

Click the Save New Payer button and repeat the above process to add each of the payers you bill to, regardless of the frequency or whether you are in-network or out-of-network.

Part 4: EDI and ERA Enrollments

Click Payers > Payer Name > Clearinghouse EDI Enrollment Status

To take full advantage of our integrated billing features, enroll to submit electronic claims and receive ERAs for each of your payers. Enrollments can be started on each payer's profile and may take a few weeks to process.

Even if you are already credentialed with a payer, additional enrollment paperwork may still need to be submitted to our clearinghouse, Change Healthcare, in order to submit electronic claims to the payer through TherapyNotes. Most payers do not require enrollment in order to be able to submit claims electronically. For those that do require special enrollment, each payer may bear slight differences on how to enroll, and instructions for enrollment can be found in the box labeled Clearinghouse EDI Enrollment Status of the payer's profile. For more information, read Electronic (EDI) Claims Enrollment.

To receive electronic remittance advice (ERAs) directly in TherapyNotes, most payers do require enrollment. To learn more, read Electronic Remittance Advice (ERA) Enrollment.

ERAs act as electronic versions of a paper explanation of benefits routed directly into your TherapyNotes account. TherapyNotes offers an assisted ERA payment posting feature which pulls information from your ERA to help you post the payment into TherapyNotes quickly. For more information on ERAs, read ERAs: Electronic Remittance Advice.

Part 5: Patient Billing Settings

Once all of your payers have been added to your account, enter relevant insurance billing information for each of your clients.

  • Click Patients > Patient Name > Billing Settings tab
  • Click anywhere on the Insurance box to edit
  • If the client uses insurance, select the Patient Has Insurance checkbox to enter primary and secondary insurance information, pre-authorizations, and additional claim information related to referrals or illness


Note: Insurance claims require you to indicate that you have your client's signature on file. This signifies that the client has provided consent for billing to their insurance company and for the insurance company to pay the provider.

For more information, read How To: Manage Client Billing Settings.


Next Steps

You've configured your settings in TherapyNotes, learned how to schedule appointments, explored our powerful note templates, and prepared your account for billing. Your account is ready to go!

Read the following articles to learn more about specific billing functions in TherapyNotes and begin billing for your services:

Previous Steps

Have more questions? Submit a request


  • Avatar
    Beth Lee

    how do I track client co-pays given that I am not in network. I want the claim form to show my total fee but also reflect clients payment. is there a way to do this?

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    Currently we only have the patients responsibility on the statement. We are working on adding more content to the statement. In the mean time you can enter anything you wish to be on the statement in the "statement comment" box before creating the statement. Anything you input into that box will appear on the statement. If you have any additional questions please contact support at 215-658-4550 or via email support@therapynotes.com

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    Dee Lundgren

    What if I'm not sure about the contracted rate. I bill first and then see what is paid by the provider. With blue cross blue shield there are many different plans. What can I do?

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    You can input the rate you bill. Once you receive payment from the insurance company you will have the option to write off the remaining balance. If you have any questions, please contact support at 215-658-4550 or via email at support@therapynotes.com. Thank you.

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    Tim Quinn

    How do I correct insurance info on a claim i just submitted electronically.

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    Please call us at 2145-658-4550 or email detailed information (including patient initials, date of service, and what needs to be fixed) to support@therapynotes.com.

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    Nikkia Day
    If a claim is processed by the insurance carrier, and is applied to the patient deductible with a zero payment, how do I post the denial to the patient's account and show them the insurance paid. And to make it show the balance as the patient's responsibility?
  • Avatar
    NIkkia, One of our support team members will contact you directly about this issue.
  • Avatar
    Kris Gooding
    I also have this question, like Nikkia...Many clients have a deductible. I need to collect payment from them, then submit a claim to the insurance payer...how do I reflect this activity on the client billing/insurance section?
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    Kris, This article contains instructions about applying deductibles: How to Apply a Deductible https://support.therapynotes.com/hc/en-us/articles/200259965 If you have a more specific question please contact the support team at 215-658-4550.
  • Avatar
    Suzi Naguib

    If a claim is processed by the insurance carrier, and is applied to the patient deductible with a zero payment, how do I post the denial to the patient's account and show them the insurance paid. And to make it show the balance as the patient's responsibility?

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    Please refer to the following article to learn how to apply a deductible:

    How to Apply a Deductible

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    Michelle Davis

    How do I add payer code to a Payer? For example, I need to add 99404 under Cigna for an EAP claim per Cigna's instruction.

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    To enter a new service code please go to your settings within TherapyNotes, click on service codes, and click on "+Add Service Code". Select the service type, enter the new service code (99404), select your duration, and the time units. Under "Rates for this service", enter your billable rate for cigna. Once the service code is added, you can then choose it when creating an appointment.

    If you have any further questions please contact support via email at support@therapynotes.com or via the phone at 215-658-4550. Thank you.

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    Becky Burch

    When primary pays, and patient has secondary how is primary payment posted do I take write off then.Then when secondary pays for 1 date of service and deny rest of out of timely how do I show that write off

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    When you enter the insurance payment from a primary payer when there is also a secondary payer on the line item, do not check the Write-Off box. This keeps the billing item open. Once you receive the insurance payment from the secondary payer enter it into TherapyNotes, but select the secondary payer from the "Payer" dropdown menu. If the secondary payer does not pay for some of the dates of service, you can allocate $0 to those dates of services and check the write-off box at that time.

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    Matthew Fulton

    How can I enter a billable Date of Service on a patient's that is not calendar/appointment related? For example, for clinician time interpreting testing data or report writing?

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    Sean Behan

    Hi Matthew,

    You can use the Psychological Evaluation note to record this information. The note template includes room to document time scoring tests and writing reports. TherapyNotes can automatically calculate the total amount of time spent as well as how many units to bill when you sign and save the note. This note is associated with the date you scheduled the original appointment on the calendar, but it can reflect time spent on other days without needing to add additional appointments.

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    Wes Goodenough

    I often have a couple request counseling where each uses their separate EAP allowance for some of the sessions. (e.g. Joe's EAP authorizes 3 sessions, and Ann's EAP authorized 3 sessions.)
    To bill each EAP appropriately I see to have to set up each partner as a separate client to bill their separate EAP. However, I lose continuity of treatment activity, as it is then divided between two clients, or I have to duplicate records from on to the other in some way.
    Is there a better way to bill to 2 separate EAP's (consecutively, not simultaneously) without losing continuity of data?

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    At this time the best method is to have both clients in as separate accounts and continue doing what you currently have set up. We value your input and will forward your feedback to management for review. If you have any questions please contact support at 215-658-4550 or via email at support@therapynotes.com Thank you!

  • Avatar
    Bella Drapkina
    Edited by Bella Drapkina