Decoding HCPCS vs CPT: Medical Codes for Pharmacies 

Pharmacies are the unsung heroes in healthcare, right? They provide essential services for the community, from safely filling prescriptions to giving health advice. To get the billing right for these services, pharmacists need to be on the ball with their accuracy. That’s where medical billing codes come into play, and two types you’ll see a lot are HCPCS and CPT codes.

So, what’s the deal with these codes? Think of them as a language pharmacies and insurance companies speak to sort out payments. CPT codes cover a wide range of healthcare services. HCPCS codes, which are more specific, cover the products and services pharmacists provide that aren’t covered in CPT codes.

Knowing the difference between HCPCS and CPT codes is essential for pharmacies. It’s similar to  having the right keys to unlock payments for your services. So, understanding these codes isn’t just about completing paperwork – it’s essential for keeping your pharmacy doors open and continuing to serve your community. Let’s break these codes down into more detail and explore why they matter so much.

What are CPT Codes?

CPT stands for Current Procedural Terminology. The CPT system, developed by the American Medical Association (AMA) and maintained by the AMA CPT Editorial panel, provides a uniform language for coding medical procedures and services

CPT codes are broken down into three categories. Most CPT codes fit into Category I, which is used to describe, report, and bill services throughout the medical industry. Category II consists of supplementary codes for performance and quality tracking. Category III consists of temporary codes used for new and emerging technologies within the healthcare industry. Pharmacies will typically use only Category I CPT codes. 

While most of these codes are for services provided by physicians, there are some instances where pharmacies use them as well. CPT codes often used by pharmacies include: 

  • 99211-99212: These codes represent an office visit or other outpatient visit for established patients that don’t require the presence of a physician. Pharmacies can use these codes to bill for services like medication therapy management. 
  • 99401-99404: Pharmacists use these codes to bill for preventive medicine and risk factor reduction services, such as lifestyle counseling. 
  • 90471-90474: Pharmacies use these codes for vaccine administration, including influenza and shingles vaccines. 
  • 99605-99607: Pharmacies use these codes for medication therapy management (MTM) services. The pharmacist provides an in–person, patient–specific medication evaluation for a new or existing patient based on factors such as the patient’s history and medication list.

What are HCPCS Codes?

HCPCS stands for Healthcare Common Procedure Coding System. Produced and maintained by the Centers for Medicare and Medicaid Services (CMS), it is divided into two subsystems. The difference between CPT codes and HCPCS codes is explained below. 

First up, Level I codes. Often referred to as CPT-4, they are the go-to codes for reporting medical services to Medicare and Medicaid. They’re pretty much the standard for most medical procedures. 

Then, there are Level II codes. Think of these as the codes that cover all the extras. They’re used for medical equipment and other services that don’t quite fit under the CPT codes umbrella.

Pharmacists use HCPCS codes to bill for a variety of pharmacy services. Some of the most commonly used HCPCS codes for pharmacies include: 

  • G0008: This code is used to bill Medicare for influenza vaccines. 
  • Q0512: This code is for pharmacy supply fee for oral anti-cancer, oral anti-emetic or immunosuppressive drug(s); for a subsequent prescription in a 30-day period.

HCPCS vs CPT Codes: What’s the Difference?

When you look at CPT vs. HCPCS codes side by side, you’ll notice they’re structured differently and serve specific purposes in medical billing. Remember, getting a good grip on how these codes vary is crucial for your pharmacy. It ensures you get properly compensated for the valuable services you offer.


One of the key differences when comparing HCPCS vs. CPT codes is that they serve different purposes in the medical billing system. CPT codes have been developed, maintained, and copyrighted to codify and report medical services. They’re designed to bill for services provided directly to patients. A physician usually provides these services. However, they can also be provided by a pharmacist in cooperation with a physician. 

The scope of the CPT system is broad, covering a large range of medical services from diagnosis to surgery and more. Some CPT codes are even used internationally. Medical providers often use these codes to describe and document the services they offer, in addition to using them for billing purposes. 

On the other hand, HCPCS codes are used to bill for a much smaller, more specific range of medical services. Since the codes are maintained by the Centers for Medicare and Medicaid Services, they are typically used to bill for services provided to Medicare and Medicaid patients. This includes billing for medical equipment and a variety of non-physician services. If your pharmacy offers in-house medical services like vaccines or counseling, you’ll use HCPCS codes to bill for them.  


One of the biggest differences you’ll notice when comparing HCPCS codes vs. CPT codes is their structure. Because these billing codes are developed and managed by two different medical agencies, they are structured very differently. 

CPT codes are entirely numeric and consist of five digits. HCPCS codes are alphanumeric, which means they use both numbers and letters. You’ll always see a letter followed by four numbers. These structures make it easy to differentiate between an HCPCS code vs. CPT code at a glance. 


Pharmacies will use both CPT and HCPCS codes when billing insurance providers. You might also use these codes when communicating with other healthcare providers to describe the services you offer. So, understanding these nuances between an HCPCS code vs. a CPT code is critical here.

Some pharmacies provide basic preventative care and other patient-facing services that do not require a physician. For example, many pharmacies provide medication consultations for their customers. These services usually fall under CPT codes. 

Pharmacies will also use HCPCS codes for a variety of services they provide. For example, HCPCS codes are often used for vaccines or for other forms of medical support, like smoking cessation. 

Why Pharmacists Need to Know the Difference

While it’s true that pharmacists don’t engage with billing codes as frequently as physicians do, they still need to understand these codes. Accurate and detailed coding of your services ensures the smooth operation of your pharmacy and minimizes any potential disruptions in billing procedures.

Failing to comprehend the distinctions between a CPT code vs. an HCPCS code could have far-reaching implications. It could not only lead to significant financial loss due to errors in billing but also tarnish your business reputation in the long term. Inaccurate coding could result in insurance companies rejecting claims, which could lead to losses for your business and dissatisfaction among your patients.

Understanding the differences between CPT and HCPCS codes is one of the primary areas that your team needs to focus on to ensure flawless operations. Here are three areas where having a solid grasp of these codes can make a difference:

Enhancing Billing and Reimbursement through Knowledge

Mastering medical codes is more than a necessity—it’s a pathway to ensuring your pharmacy’s billing is seamless and insurance reimbursements are timely. By accurately communicating the services provided through these codes, you unlock the door to prompt and correct reimbursements from insurance providers.

Getting familiar with the difference between CPT and HCPCS codes not only helps avoid billing mistakes but also opens up opportunities for your pharmacy to receive payments more quickly and accurately. This knowledge is especially beneficial when dealing with Medicare and Medicaid patients, requiring specific coding that, when mastered, ensures your services are reimbursed properly. Accurate billing not only supports your pharmacy’s financial well-being but also upholds high standards of integrity and avoids the pitfalls of billing inaccuracies.

Compliance and Auditing as Opportunities for Growth

Understanding and applying the correct billing codes is a cornerstone of compliance with healthcare regulations such as HIPAA. It positions your pharmacy as a responsible and trustworthy entity, laying a strong foundation for operational excellence.

Adhering to the right HCPCS and CPT billing codes not only streamlines regulatory compliance but also significantly reduces the risk of complications during audits. It’s a proactive measure that not only avoids fines or legal issues but also enhances your pharmacy’s reputation, building trust and confidence among your patients. Embracing these practices not only minimizes the risk of audit failures but also sets your pharmacy apart as a beacon of reliability and compliance.

Building Bridges with Efficient Communication

Utilizing the correct billing codes does more than facilitate transactions—it fosters efficient and effective communication within the healthcare ecosystem. This clarity in communication makes your pharmacy a preferred partner for physicians, enhancing your reputation and potentially leading to an increase in patient referrals.

Moreover, accurate documentation and billing code usage can significantly improve how you communicate with patients regarding their insurance coverage and reimbursement questions. This transparency and accuracy in communication not only elevate patient trust but also contribute to a smoother, more positive healthcare experience.

Embracing the intricacies of billing codes not only safeguards your pharmacy’s financial health but also positions it as a key player in the healthcare community, with the potential to unlock increased revenue and growth opportunities.

Get Started with DocStation Today

Understanding how HCPCS and CPT codes work is key to reducing billing errors and keeping your pharmacy running smoothly. However, when you’re busy juggling so many important patient services each day, it can be difficult to stay on top of your medical billing. DocStation is an all-in-one pharmacy solutions platform. It allows you to keep track of important medical codes and streamline the entire billing process. You’ll save time and stay organized. Reach out today to see how DocStation can help your pharmacy.