Ultimate Guide to Pediatric CPT Codes

Last Updated on September 16, 2025

Coding for pediatrics isn’t just about plugging in numbers. Each CPT code tells a story about how a child was cared for, whether it’s a first well visit, a vaccine that keeps them safe, or a NICU stay that requires critical care. Pediatric coders have to balance preventive services, acute visits, screenings, and hospital care, all while staying sharp on documentation rules and payer quirks.

Here’s a detailed breakdown of the common pediatric CPT Codes practices use every day, the mistakes that slow down claims, and the habits that help keep reimbursement smooth.

Preventive and sick visits

Preventive CPT codes (99381–99395) cover well-child visits from infancy through adolescence. These are not generic “physicals.” They’re structured visits that follow age-based guidelines, including a comprehensive history, exam, anticipatory guidance, and counseling for parents or guardians. The code chosen depends on the patient’s age and whether they’re new or established.

Sick visits use the E/M office/outpatient CPT codes (99202–99215). Since the 2021 changes, these codes are based on medical decision making (MDM) or time spent, not on exam bullet points. This shift is especially useful in pediatrics where complex counseling or coordination often takes more time than a quick physical check.

Both sets of codes can appear on the same day. For example, a child may come in for a scheduled well visit but also have ear pain. The preventive visit (99391) covers the well exam, while a separate problem-oriented E/M (99213) can also be billed with modifier 25. The documentation needs to clearly separate the two services, think of it as two mini notes in one encounter. Practices that don’t document these distinctions well often see preventable denials pile up. That’s why strong pediatric coding habits go hand in hand with denial management strategies.

Key tip: Always create a separate assessment and plan for the acute issue. Even a single line, “Acute otitis media treated, not part of preventive service”, strengthens the claim. Without this, payers often deny the additional E/M.

Immunization CPT Codes

Vaccines are the heartbeat of pediatrics, and vaccine billing is one of the most error-prone areas. Every vaccine has two parts: the product code (for the vaccine itself) and the administration code (for the work of administering and counseling). Miss either part and reimbursement won’t be complete.

For children up to 18 years of age, when counseling is provided, the correct CPT codes are:

• 90460 — first component of each vaccine product
• +90461 — each additional component within that product

A “component” is an antigen that targets a specific disease. A DTaP vaccine, for example, has three components: diphtheria, tetanus, and pertussis. That means one unit of 90460 for the first component, plus two units of 90461 for the others.

When counseling isn’t provided, or when the patient is over 18, use the 90471–90474 series, which is based on route of administration and the number of vaccines.

Example: A 2-year-old receives MMR (3 components), DTaP (3 components), and HepA (1 component). That equals three units of 90460 (first component for each vaccine) and four units of 90461 (two for MMR, two for DTaP). Missing even one 90461 leads to underbilling.

Common pitfalls:

• Documenting vaccines but forgetting to note counseling.
• Billing 90460 only once for an entire visit instead of per product.
• Leaving out product codes and only submitting admin codes.
  

Smart habit: Add a standard line in your vaccine note: “Counseled caregiver, administered [vaccine names], components counted and documented, VIS provided, patient tolerated well.” That one sentence protects reimbursement and audit readiness. It’s also worth noting that missed vaccine components can quickly snowball into underpayments, which later need to be tracked in AR follow-ups. A clean vaccine workflow helps cut down those rework cycles

CPT Codes for Pediatric screenings

Screenings are a big part of preventive care. They’re often quick, but if not coded and documented correctly, the practice loses out on revenue.

Developmental and behavioral screening CPT Codes

• 96110 — standardized developmental screening (like ASQ or PEDS)
• 96127 — brief behavioral or emotional screening (such as PHQ-9 or GAD-7)

These CPT codes should always include the tool name, the score or result, and the next step. Simply writing “screened, normal” isn’t enough for payers. A stronger line would be: “ASQ-3 completed, communication domain below cutoff, referred to speech therapy.”

Vision screening

• 99173 — quantitative visual acuity screening, typically with Snellen or similar charts
  Instrument-based screenings, such as photoscreening, may have different codes depending on payer policy. Always specify the method used.

Hearing screening

• 92551 — pure-tone screening (basic office test)
• 92587/92588 — otoacoustic emissions (limited or comprehensive)
• 92567 — tympanometry, used when middle ear issues are suspected

Coverage for advanced hearing tests can vary, so many practices keep a payer-specific matrix to know which insurers reimburse OAEs in primary care.

Practical tip: Build a documentation shortcut into your EMR: Tool – result – plan. Example: “99173 vision screen: 20/30 OU, plan: recheck next year.” That one-line formula works across screenings and satisfies payer requirements. Screenings are also where eligibility checks matter, if coverage for vision or hearing tests isn’t verified ahead of time, claims may bounce back, creating unnecessary AR delays.

Newborn and critical care Codes

Hospital care for newborns and critically ill children has its own coding families, and they look very different from office visits.

Newborn care codes

• 99460 — initial hospital or birthing center care, per day, for a normal newborn
• 99461 — initial care provided outside the hospital
• 99462 — subsequent care for a normal newborn
• 99464 — attendance at delivery
• 99465 — resuscitation of newborn at delivery

Critical care CPT codes

• 99468–99469 — neonatal critical care (per day)
• 99471–99472 — pediatric critical care (per day)
• 99475–99476 — subsequent intensive care for infants and children
  

A key point is that many routine tasks in NICU and PICU—like pulse oximetry, ventilator management, or certain lab interpretations, are bundled into the critical care codes. That means they shouldn’t be billed separately. Adding them as extra services often leads to denials or even audit flags.

Best practice: Keep a bundled checklist in your NICU or PICU documentation template. If a service feels “routine” or supportive, it’s probably included in the daily critical care code. Because NICU and PICU billing is high-dollar, even small coding errors can lead to significant underpayments. Many practices build internal audits to catch those issues before they affect cash flow.

Important Modifiers in Pediatric Coding

Modifiers are small two-digit numbers, but in pediatric Coding  they can make or break a claim.

• Modifier 63 — used for procedures performed on infants weighing less than 4 kilograms. It applies only to surgery codes (20000–69999). Always document the infant’s exact weight on the date of service.
• Modifier 25 — used when a significant, separately identifiable E/M service is provided on the same day as another service, like a well-child visit plus treatment for strep throat.
• Modifier 59 — used for distinct procedural services when no other modifier applies. Overuse of 59 is a red flag for auditors, so use it sparingly and only when services are truly separate.

Quick habit: Teach providers to write in plain language when a separate service was performed: “In addition to preventive services, evaluated and treated acute pharyngitis.” That one line justifies modifier 25 cleanly. Modifiers are also a frequent target in payer audits and is just as important as choosing the right CPT.

Telemedicine updates

Virtual visits remain common in pediatrics, but payers differ on how they want them reported. Some reimburse for audio-video only, while others allow audio-only visits. Codes may be the same as in-person office visits (99212–99215), but the place of service and modifiers matter.

The safest approach is to keep a payer-specific cheat sheet that lists which visit types are covered, what place of service to use, and which modifiers (like 95 or FQ/FR) apply. This prevents mismatched claims that clog up accounts receivable.

Tip for documentation: Always note the type of telehealth visit (video or audio), who was present (child, parent, both), and how much time was spent. These details make coding defensible.

Bringing it together

Here’s how all these rules come together in practice:

Example 1: 6-month well visit with vaccines and an ear infection

• 99391 (well visit)
• 96110 (developmental screen)
• 90460 x2 + 90461 units for vaccines with counseling
• 99213-25 for the acute ear infection, with a separate assessment and plan

Example 2: NICU day with procedures

• 99468 (neonatal critical care)
• Central line insertion billed separately with modifier 63 if infant weighed under 4 kg
• Routine monitoring like pulse ox not billed separately because it’s bundled