COVID-19 Vaccines: Plan, Configure, Order, Administer, and Bill

You can use PCC EHR to order, administer, and track COVID-19 vaccines, either for pediatric patients or as part of a COVID-19 vaccine clinic for older patients. Read below to learn how to sign your practice up, plan for a vaccine clinic, configure your PCC system, and how to order, administer, and track COVID-19 vaccination.

Live Community Forum: To learn more, watch a recording of PCC’s Pediatric COVID-19 Vaccine Roundtable from 2021-11-05.

Get Signed Up and Plan for COVID-19 Vaccinations

Pediatric practices across the country are now administering adult vaccinations and the age 12+ Pfizer-BioNTech COVID-19 vaccine. In early November 2021, ACIP and the FDA are expected to issue Emergency Use Authorization (EUA) for a COVID-19 vaccine for children ages 5-11. President Biden intends for pediatric practices to play a key role in the vaccination of young patients.

How can your practice get started?

  • Register to Administer COVID-19 Vaccines: If you haven’t already registered to administer the COVID-19 vaccine, you can find your state specific registration details at the AAP’s State COVID-19 Vaccine Provider Registration Resources page.

  • Evaluate Your Active Patient Population for Target Age Groups: Use PCC’s Report Library to estimate patient populations. For example, how many 5-11 year olds have visited your practice in the past three years? Don’t forget to consider children who will be turning 5 in the upcoming months. Consider also contacting 12 to 21 year olds, and beyond, who visit your practice: while families may have already received vaccination elsewhere, your practice can help fill in the gaps.

  • Plan Your Practice's Vaccine Clinic: Develop a plan to administer the vaccine with your practice. Consider holding a vaccine clinic and also offering COVID-19 vaccination during regularly scheduled visits. PCC has documentation and a blog article about running mass vaccine clinics.

  • Communicate With Families: Use Broadcast Messaging to communicate your plan early to your patient families. This will help reduce phone calls to your office and encourage families to plan how and when they will get their children vaccinated.

  • Add Immunization Billing Codes and Make Other Configuration Changes to Your PCC System: Use the links and the procedure below to add billing procedures to your system and set up orders and chart note protocols for quick and easy administration. PCC Support can help you with every step of the process.

  • Create or Obtain a Consent Form: Your practice can create your own consent form, or there may be a standard one available from your state. PCC has heard from pediatricians who use the new Massachusetts COVID-19 Vaccine for 5-17 Years form and Oregon’s Pfizer Minor Consent Form.

  • Obtain VIS Forms (EUA Fact Sheets) at CDC.gov or through FDA: For COVID-19 vaccines in 2020-2021, there is no formal VIS form. Instead, manufacturers work with the CDC to provide Emergency Use Authorization Fact Sheets. In November of 2021, the FDA released Pfizer 12+ Fact Sheets and Pfizer 5-11 Fact Sheets.

Understand the Details and Codes for Each Vaccine

Before you set up a new vaccine in PCC’s system, you should review and understand the details of the immunization. You will need to know the manufacturer and their MVX code (such as PFR, for Pfizer), the dose amount, the CVX Code for the vaccine, the National Drug Code (NDC) for the vial, along with the CPT code you will use for billing. Your practice will also want to review diluent information for administration and obtain VIS forms.

In the fourth quarter of 2021 and into 2022, PCC believes pediatric practices are most likely to administer the following two vaccines:

Ages Approved by EUA Manufacturer (MVX) Long Name EUA Fact Sheet (VIS) NDC of Vial CVX Dose Amount Vaccine Billing Code Admin 1st dose Admin 2nd dose Admin 3rd dose Booster
12+ Pfizer (PFR) SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 30 mcg/0.3 mL dose COMIRNATY and Pfizer-BioNTech COVID-19 Vaccine EUA Fact Sheet 59267-1000-01 208 0.3mL 91300 0001A 0002A 0003A 0004A
5-11 Pfizer (PFR) SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 10 mcg/0.2 mL dose, tris-sucrose formulation COMIRNATY and Pfizer-BioNTech COVID-19 Vaccine EUA Fact Sheet 59267-1055-01 218 0.2mL 91307 0071A 0072A

You can obtain full information from resources provided by the AAP, CDC, and the AMA:

Configure PCC EHR for COVID-19 Vaccines

Read below to learn how to add a COVID-19 vaccine to your PCC system. Contact PCC Support for assistance with any of these steps.

In addition to adding a vaccine that you will administer, you can use the steps below to add vaccines that your practice will track but will never administer.

See More About Adding an Immunization: For more screenshots and help with these configuration tools, see the main Add and Configure Immunizations in PCC reference article.

Create Immunization Entries in Your Practice’s Procedures Table

First, create procedure entries for the vaccine in the Procedures table in your practice’s Table Editor (ted). If you’ve never done this before, contact PCC Support and we will walk you through the process. (You can see more screenshots on the main Add Immunizations article.)

  • Procedure Name: You can name procedures anything that will be useful for your practice. As there will be several different COVID-19 vaccines coming into use in 2021, PCC recommends a naming convention that identifies the manufacturer of the vaccine. If you will be administering two different dosages of the Pfizer vaccine (for example, 0.3ml for older patients), you may want to incorporate the dosage or age range into the title of the procedure.

  • Accounting Type: Billable procedures you perform in your practice should have an accounting type of “Revenue”.

  • Procedure Group: The Procedure Group field is a customizable value used for reporting purposes; it does not affect billing or how a procedure is ordered or completed. Select an appropriate Procedure Group, such as “Immunizations”.

  • TOS: The Type of Service should read “Medical Care” for all immunizations or medications you administer.

  • Units: Enter one (1) unit. The Procedures table lists the smallest, standard administered value for the vaccine.

  • NDC: Enter the National Drug Code for the COVID-19 vaccine. You can use the table provided above or the CDC’s informational table, but you should check the labeling on the vaccine vial itself when it arrives at your practice. You can also cross-reference the National Drug Code Library.

    From the Vial, Not the Box: You should enter the NDC code printed on the smallest administered dose, such as the specific tube, vial, or pouch that contains the vaccine or medication. Do not use the NDC code printed on a box or carton that contains more than one dose.

  • Dose Amount and Dose Units: Enter the dose amount and dose units found on the vial, pouch, or tube that you administer. For example, the Pfizer COVID-19 vaccine is administered as 0.3 mL for older patients, so you would enter “0.3” and “mL”. It is expected that the 5-11 vaccine will be a 0.2mL dose. If you are administering different doses, you should set up different entries in your Procedures table.

  • Procedure Code or CPT: Use the table above or the CDC or AMA links to locate the billing procedure code and enter it in all schedules. PCC does not provide or distribute CPT codes, and can not add this information to your system. Enter the same code for all schedules. PCC includes optional schedules in order to support “local codes”, which are no longer part of the claim standard. However, if your practice has a schedule specifically configured for Medicaid billing, and your state Medicaid program requires a modifier, you can enter the full code + modifier in the “CPT” field for that schedule.

  • Price: Enter a price for the procedure in the fields for each schedule. As of 11-2021, PCC expects most practices should enter a $0.00 price for COVID-19 vaccines, though your situation may vary. For example, CMS publishes a $0.01 price, and some payers may not be able to process $0.00 charges on claims. In general, procedure prices should be identical in all fields, though a practice can use different fee schedules for TOS payment or Medicaid vaccines (VFC). The examples in the image above are for illustration only and are not fee suggestions.

Add the New Immunization Administration Procedures to Your Procedures Table

Next, clone an existing Immunization Administration procedure and adjust the description and code for administration of the COVID-19 vaccine. Each administration for each vaccine has a unique code! See the table above.

PCC expects most pediatric practices will be tracking five or six different administration billing codes, including the first and second dose of the expected Pfizer 5-11 vaccine and administration and followup shots for the 12+ vaccine.

What should I charge for COVID-19 immunization administration?: We recommend you check with your payers to determine expected payment for COVID-19 vaccine administration codes. Note that Medicare presently pays $40 for each administration and some private payers or individual states may be paying more.

Create or Adjust Entries in Your Immunization Manufacturers Table

Next, review and update your practice’s Immunization Manufacturers table in the Table Editor (ted).

Your table may already include Moderna, for example, but you may need to add Pfizer.

Create Entries in the Immunization and Disease Table

PCC Support will complete this step for you. Contact them at support@pcc.com or 1-800-722-1082.

The Immunization and Disease table handles how specific immunization procedures in your Procedures table align with vaccination and/or diseases. Contact PCC Support for assistance.

Configure Your System to Display the Vaccine and to Print It on Immunization School Forms

PCC Support will complete this step for you. Contact them at support@pcc.com or 1-800-722-1082.

Your Client Advocate or other PCC support team member will add the new vaccine to four “under-the-hood” configuration tables, work with you to make adjustments to your printable immunization school form(s), and work with you to test the configuration and make sure that the new vaccine appears correctly in PCC EHR.

Add a COVID-19 Immunization Order to Specific Chart Note Protocols

Use the Protocol Configuration tool to add the COVID-19 vaccine to the Immunizations component for specific chart note protocols.

A clinician can always search and find any immunization order. You can save clinicians’ time by putting specific immunizations right on your practice’s chart notes, so they will be available with a single click.

Add Catch-Up Imms, Flu Shots, and More: The AAP recommends practices take advantage of every encounter to get patients caught up on immunizations and offer flu shots. As you adjust your protocols for a COVID-19 vaccine clinic, consider other components and immunizations you can add to help your clinicians during the visit.

Map Z23 and Billing Procedures to the COVID-19 Immunization Order

When a clinician clicks “Order” next to a COVID-19 vaccine, PCC EHR can automatically place diagnosis and procedure billing codes onto the encounter for billing. Whenever you add a new vaccine, use the Billing Configuration tool to map precisely which codes should be triggered by that order.

In the example above, the practice has mapped the COVID-19 (Pfizer, 5-11) immunization order to a Z23 diagnosis, a billing CPT code, and two specific immunization administration codes.

Customize How the Immunization Appears in the Patient’s Chart

Use the Immunization Configuration tool in PCC EHR to configure the order that immunizations appear in a patient’s Immunization History. Use the same tool to set whether or not the immunization will always appear in a patient’s chart or will only appear if they have had a dose.

Click and drag to rearrange how immunizations appear in a patient’s chart. Click the “Display” checkbox next to all immunizations you would like to appear in a patient’s Immunization History, even if they have never received a dose.

Always Display: In a patient’s chart, the Immunization History will display all immunizations that a patient has received. You can also configure an immunization to appear on every patient’s record, even if they have never received a dose. For example, since all patients should receive an IPV, most practices select “Display” next to “IPV” in the Immunization Configuration tool. In contrast, a practice might sometimes administer a cholera vaccine, but would only need it to appear in the patient’s record if a patient received it. They therefore would not check “Display” next to Cholera.

Create a COVID-19 Vaccination Pre-Registration Form in the Patient Portal

Your practice can create a pre-registration template in the patient portal, so parents can answer COVID-19 vaccine registration questions quickly and easily on their smart phone. You can use these forms to gather information ahead of a vaccine clinic, or send the form to families after they’ve schedule their appointment.


To learn about patient portal templates, read Configure Your Patient Portal Message Templates.

To see what other practices have done, download Portal Message Template – 5-11yr COVID Shot Pre-registration.

Add Incoming COVID-19 Vaccine Lots in the Lot Manager

When the vaccine arrives at your practice, add it to the Lot Manager in PCC EHR.

You can use a barcode scanner to enter information, or enter it manually. Use the documentation that accompanies the vaccine and/or the CDC links at the top of this article to learn more about dosage, diluent, and NDC code information for each vaccine. Note that cartons and vials have different NDC codes.

Order and Administer a COVID-19 Vaccine

Use the Immunizations component on the chart note to order and administer a vaccine.


When you chart the administration of any immunization, you can select a lot, select which VIS/EUA Fact Sheet you provided, and then indicate that you administered the shot or that it was canceled or refused. PCC EHR will enter your practice’s default or most recent shot information for some fields.

Provide an EAU Fact Sheet Instead of a Vaccine Information Sheet (VIS)

In PCC EHR, you can indicate which VIS you provided to a patient. There are currently no VISs for COVID-19 vaccines. Instead, the CDC and FDA are working with vaccine manufacturers to prepare and share Emergency Use Authorization Fact Sheets to recipients. In PCC EHR, the EUAs will appear in the drop-down menu instead of the VIS.

  • CDC EUA Fact Sheets: Your practice can download the EUA Fact Sheets for all COVID-19 Vaccines on the CDC’s web site.

  • FDA's New 12+ and 5-11 Fact Sheets: In November of 2021, the FDA released Pfizer 12+ Fact Sheets and Pfizer 5-11 Fact Sheets.

  • Distribute EUA Fact Sheets as QR Codes: In addition to handing parents a printed copy of the EUA Fact Sheet, your practice can print and display QR codes. Parents can then use their smartphone camera to jump directly to the web site.

  • The CDC's COVID-19 Vaccine Handout: In addition to the EUA Fact Sheet, your practice may choose to distribute your own materials or the CDC’s What to Expect after Getting a COVID-19 Vaccine document. You can find this document on the CDC’s information pages for COVID-19 vaccines approved in the United States.

    Bill for COVID-19 Vaccines

    When your practice clicks “Order” next to a COVID-19 vaccine, your practice’s configured billing diagnoses and procedure codes will appear on the Bill screen automatically.

    A clinician will see the codes when they prepare the encounter for billing.



    You can make any adjustments needed. (Note that the above example does not include a visit code or other billing codes that might be part of a typical encounter.)

    After the clinician has made the encounter ready for billing, the biller can post the charges from the Schedule screen in PCC EHR.


    As they post charges, the biller can review and adjust patient information, along with the diagnosis and procedure codes.

    What Billing Diagnoses and Procedures Do I Use for a COVID-19 Related Encounter?: While circumstances will vary, PCC has an overview of Coding and Billing for a COVID-19 Related Encounter.

    Review and Understand COVID-19 Immunization Forecasting Details

    In 2021, PCC anticipates immunization forecasting for COVID-19 will be inconsistent. There are numerous vaccines in play, each with different dosage rules. Federal and State governments may decide to advise clinicians to ignore some periodicity requirements, and those requirements are changing rapidly.

    PCC is working with our immunization forecasting vendor to deliver updated forecasting as soon as it is available. In the meantime, you may only see a COVID-19 line in the Immunization Forecasting component if a patient has (for example) received a first dose of a multi-dose vaccine. Support for dose schedules for each approved vaccine is planned.

    Can My Pediatric Practice Become a COVID-19 Vaccine Site for Adult Patients?

    Many pediatric practices are working with their local health department in order to administer COVID-19 vaccines to both children and adults.

    PCC has worked with practices to help them get set up, and you can read more at COVID-19 Vaccine: What Pediatricians Need to Know.

    Become a Medicare Provider

    If you plan to administer the COVID-19 vaccine to Medicare patients, or see Medicare patients for other reasons, you may decide to register as a Medicare provider.

    The Federal Government is working to expedite the Medicare enrollment process in order to make sure more clinicians are able to see Medicare patients for COVID-19 related needs and/or to administer the COVID-19 vaccine. Clinicians need to enroll in Medicare in order to bill for encounters with Medicare patients.

    You can learn about the expedited enrollment process here: CMS (https://www.cms.gov/files/document/provider-enrollment-relief-faqs-covid-19.pdf). Once a clinician is enrolled, they can see Medicare patients and administer the COVID-19 vaccine. After the pandemic, a clinician would have to complete the full enrollment process.

    Medicare does not accept paper claims, and signing up for electronic claim submission with Medicare is a separate process. PCC’s EDI experts can assist you with setting up claim submission. This process has not been expedited in the same way as enrollment, and PCC anticipates initial claim submission could take up to a month.

    • Last modified: November 9, 2021