In adults, the presence of the BRAF (V600E) mutation in papillary thyroid cancer (PTC) has been demonstrated to be strongly associated with aggressive cancer-cell characteristics and poor patient prognosis. In contrast, the frequency of this mutation in pediatric PTC has undergone limited study, and the few available estimates range from 0 to 63%. Furthermore, the role of the BRAF (V600E) mutation in pediatric PTC is controversial; thus, the present study aimed to investigate the prevalence and role of the BRAF (V600E) mutation in 48 pediatric patients with PTC, aged 3-13 years. Of these patients, 41 were diagnosed with classic PTC, five were found to have a follicular variant of PTC, and two to exhibit a diffuse sclerosing PTC variant. The BRAF (V600E) mutation was identified to be present in 35.4% of the 48 analyzed patients, and in 41.5% of the patients diagnosed with classical PTC. Furthermore, the presence of the BRAF (V600E) mutation was found to be associated with a patient age at diagnosis of less than ten years (P=0.011), the performance of a thyroidectomy (P=0.03), exhibited tumor multifocality (P=0.02) and/or extra-thyroidal invasion (P=0.003), and both a low MACIS (Metastases, Age, Completeness of resection, Invasion, Size)(P=0.036) and AMES (Age, Metastasis, Extent of tumor, Size)(P=0.001) score. Together, these data suggest that the presence of the BRAF (V600E) mutation may be negatively correlated with partial aggressive clinicopathological features of pediatric PTC.