Vaccine Billing & Coding Updates for 2025

Tired of the headaches that come with vaccine billing and coding? Don’t sweat it, our 2025 vaccine billing and coding updates guide is here to make things easier, more efficient, and even a little enjoyable. 

We’ve got the latest CPT updates for SARS-CoV-2, influenza, pneumococcal, meningococcal, and other vaccines, all packed into a single resource to help you nail compliance and boost revenue. 

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Table of Contents

Why Vaccine Coding Is a Big Deal in 2025?

Vaccine billing and coding can significantly impact practice revenue and compliance. The 2025 updates introduce critical changes, including deleted, revised, and new CPT codes for SARS-CoV-2, influenza, pneumococcal, and other essential vaccines. 

virus image vaccine billing and coding updates

Luckily, you don’t have to do it alone.  

Neolytix brings you a detailed overview of these updates to ensure integration into your billing processes.   

Whether you manage a small clinic or a large healthcare organization, accurate vaccine coding is essential for maximizing reimbursement and maintaining regulatory compliance 

Why These Vaccine Coding Updates Are Worth Your Attention?

Proper vaccine coding isn’t just about compliance; it directly affects your practice’s financial health and patient care delivery. Below is a breakdown of how these updates drive success for your practice: 

Key Benefit  Why it Matters 
Reduce Revenue Loss  Avoid denied claims and underbilling by staying ahead of coding changes. 
Stay Compliant  Align with AMA guidelines and prevent costly penalties or audits. 
Enhance Patient Care  Accurate coding improves vaccine administration workflows, ensuring timely patient care. 
Maximize Reimbursement  Reflect new vaccine formulations and dosages for precise billing and increased revenue. 

By prioritizing accurate vaccine coding, your practice not only secures financial stability but also enhances the quality of care provided to patients 

Key Updates for 2025

      A. Deleted Codes (Outdated codes no longer recognized for reimbursement.)     
  • 90630 (Influenza virus vaccine, quadrivalent, live) 
  • 90654 (Influenza virus vaccine, trivalent, split virus) 
  • 93890 (No longer applicable) 
  • 96003 (Medical service procedure no longer in use) 
  • 96040 (Genetic counseling, deleted and replaced with new codes) 
  •  (SARS COV-2 Vaccines) 91300—91317  
  • SARS COV-2 Admin codes- 0001A-0004A, 0051A-0054A, 0121A-0124A, 0071A-0074A, 0151A-0154A, 0081A-0083A, 0171A-0174A, 0011A-0013A, 0064A, 0134A, 0141A-0144A, 0091A-0094A, 0021A-0022A, 0031A-0034A, 0041A-0042A, 0044A, 0104A, 0111A, 0113A, 0164A  
  B. Revised Codes (Updated dosages, ingredients, or administration guidelines.)   
  •  91304: SARS-CoV-2 vaccine, recombinant spike protein nanoparticle, saponin-based adjuvant, 5 mcg/0.5 mL 
  • 90661: Influenza vaccine, trivalent (ccIIV3), derived from cell cultures 
  C. New Codes   
  • 90593: Chikungunya virus vaccine, recombinant, for intramuscular use This vaccine is used to prevent Chikungunya fever, a viral disease transmitted by mosquitoes.  
  D. Resequenced codes     
  • 90480: Immunization administration by intramuscular injection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (coronavirus disease [COVID-19]) vaccine, single dose  
  • The code range 91300 – 91317 has been replaced by 91318 – 91322 with proper sequencing.  
  • 90695: Influenza virus vaccine, H5N8, derived from cell cultures, adjuvanted, for intramuscular use  
  • 90684: Pneumococcal conjugate vaccine, 21 valent (PCV21), for intramuscular use  
  • 90637: Influenza virus vaccine, quadrivalent (qIRV), mRNA; 30 mcg/0.5 mL dosage, for intramuscular use-  
  • 90638: Influenza virus vaccine, quadrivalent (qIRV), mRNA; 60 mcg/0.5 mL dosage, for intramuscular use   
  • 90624: Meningococcal pentavalent vaccine, Men B-4C recombinant proteins and outer membrane vesicle and conjugated Men A, C, W, Y-diphtheria toxoid carrier, for intramuscular use  

Common Vaccine Billing Denials & How to Solve Them

Vaccine billing denials can be frustrating and costly, but understanding why they happen and how to address them can make a huge difference for your practice’s cash flow.    Here’s a breakdown of the most common vaccine billing denials and smart solutions to prevent them from becoming a recurring issue: 
Common Denial  Cause  Solution 
Code mismatch  Outdated or incorrect CPT codes used  Use real-time CPT code monitoring and integrate automated systems for updates. 
Invalid Dosage  Incorrect vaccine dosage billed  Automated dose verification and EHR synchronization 
Lack of Medical Necessity  Insufficient documentation or improper coding  Ensure proper documentation and coding alignment with payer requirements 
Missing NDC (National Drug Code)  Omitted or incorrect NDC entered  Implement automated NDC checks before claim submission 
Duplicate Billing  Same vaccine billed multiple times  Automated claim scrubbing and reconciliation 
Payer-Specific Requirements  Variations in payer vaccine coverage policies  Neolytix manages payer communication and compliance 
Untimely Filing  Delays in claim submission  Implement automated claim submission workflows to avoid delays 

By addressing these denials proactively, your practice can simplify billing processes, reduce revenue loss, and boost reimbursement rates. Neolytix’s expertise ensures you stay ahead of challenges, making vaccine billing a stress-free experience. 

Practical Coding Examples: Real-World Scenarios Made Simple

Understanding vaccine coding can feel overwhelming, but real-world examples make it easier to grasp. Here are some common scenarios to illustrate proper code assignment and ensure your claims are spot on: 

Administering a Flu Vaccine with an Office Visit 

Scenario 

A patient comes in for their annual flu shot and discusses mild cold symptoms during the visit. 

 Coding  

  • CPT Code for the flu vaccine (e.g., 90686 for quadrivalent flu vaccine). [1] 
  • Administration code (e.g., 90471 for the first vaccine). 
  • Modifier 25 with the E/M code to signify a separate, significant service during the same visit.
     
Billing for Multiple Vaccines in One Visit  

Scenario  

A child receives a pneumococcal vaccine and a meningococcal vaccine during the same appointment. 

 Coding  

CPT Codes for each vaccine (e.g., 90732 for pneumococcal and 90734 for meningococcal). [1] 

Administration codes (e.g., 90471 for the first vaccine and 90472 for the additional vaccine).
 

The Role of Documentation: Accuracy is Key

When it comes to vaccine billing, documentation is more than a formality, it’s the backbone of accurate coding and successful claims. Missing or incomplete records can lead to denials, delayed reimbursements, or even compliance issues. 

Tips for Better Documentation:

approved image vaccine billing and coding updates
  • Record the vaccine type, administration details, and lot numbers consistently. 
  • Include the patient’s medical necessity for receiving the vaccine as part of the visit summary. 
  • Double-check for alignment with payer requirements before submitting claims. 

Remember, the more precise your documentation, the easier it becomes to resolve disputes or justify claims with payers. 

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Partner with Neolytix for 2025 and Beyond

Why stop at vaccine coding? Neolytix brings over 12 years of experience helping practices like yours thrive. From revenue cycle management and medical billing to payor contract negotiation and credentialing, we’re your go-to partner for end-to-end healthcare solutions. 

Don’t forget to check out our other 2025 guides, covering Pain Management, Occupational Therapy, and more. 

Check out our other 2025 guides today!  Guides Catalog 

Let’s make this your best year yet. 

Contact Neolytix today to get started 

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