Background Pediatric patients present with thyroid nodules less often than adults, but the rate of malignancy is much higher. This study was designed to determine the ability of fine-needle aspiration cytology (FNA) to diagnose accurately and facilitate management of thyroid neoplasms in pediatric patients. Methods A retrospective study revealed 110 patients <19 years old who had undergone thyroid surgery and FNA biopsy at two academic institutions over the last 28 years. FNA sensitivity for diagnosing papillary thyroid cancer (PC) and follicular neoplasm (FN) was investigated. Results Of 110 patients who presented for surgery, 27 had PC and 33 had a FN: 4 follicular carcinomas (FCs) and 29 follicular adenomas (FAs). Among the PCs patients, the FNA results were as follows: 1 (4%) nondiagnostic, 6 (22%) atypical, 2 (7%) benign, and 18 (67%) malignant lesions. The sensitivity of a malignant FNA was 90% for diagnosing a PC. Sensitivity of an atypical FNA was 75% for FCs and 69% for FAs, giving an overall FN sensitivity of 70%. Of the atypical FNA readings, 60% had confirmed histological atypical features, and 19% were malignant. In 95% of the malignant FNA reports, final histology confirmed PC, resulting in a positive predictive value of 95%. Conclusions FNA biopsy can reliably diagnose malignancy in pediatric thyroid patients and should be used as a standard technique to indicate surgical treatment. Atypical or suspicious FNA results do not predict cancer effectively, confirming the current accepted practice for adults that diagnostic excision is required to exclude malignancy in pediatric patients.