Purpose Treatment of pediatric papillary thyroid cancer (p-PTC) often follows adult guidelines, including total thyroidectomy for tumors > 1 cm. This study examined the association between operation type and overall survival (OS) for tumors > 1 cm in size in the pediatric population. Methods Patients ≤ 21 years of age with primary papillary thyroid cancer > 1 cm were reviewed from the National Cancer Data Base (NCDB) from 1998 to 2011. Kaplan-Meier analysis followed by Cox proportional hazard models estimated the impact of total thyroidectomy (TT) vs. partial thyroidectomy (PT) on overall survival. Models were adjusted for patient, tumor, and treatment factors. Results 3,861 cases (3474 TT, 387 PT) were included. Estimated 15-year overall survival was 96.10% after TT and 96.18% after PT (p = 0.0855). In multivariate analysis of 3173 patients, only lowest socioeconomic level (HR 4.93, p = 0.001) and unfavorable histology (HR 6.11, p = 0.016) were associated with worse OS. Survival for patients undergoing TT was not statistically improved over those undergoing PT (HR 0.81, p = 0.694). Conclusion p-PTC > 1 cm has an excellent 15-year overall survival. Treatment with TT did not have an improved OS compared to PT. Lower socioeconomic status and unfavorable histology were associated with decreased OS.