The management of thyroid nodules is guided by the cytological classification provided by The Bethesda System for Reporting Thyroid Cytology. Notably, the biology of thyroid tumors in pediatric patients differs from that in adults, and there is limited research focused on pediatric cases. This study aimed to assess the effectiveness of the Bethesda system in pediatric patients treated at the largest tertiary pediatric thyroid center in Poland between 2015 and 2023. A retrospective analysis was conducted on 566 patients with thyroid nodules, of whom 555 underwent fine-needle aspiration biopsy (FNAB). A total of 217 patients underwent thyroid surgery. Of these, 206 had previously undergone FNAB with cytological evaluation at our center, while 11 patients underwent thyroid surgery due to a RET mutation or the need for an extended procedure. The initial FNAB results showed distribution across Bethesda categories as follows: 7.6% for category I, 54.6% for category II, 20.9% for category III, 4.1% for category IV, 7.6% for category V, and 5.6% for category VI. Among patients who underwent surgery, the distribution of Bethesda categories I through VI was 2.9%, 25.2%, 29.1%, 8.3%, 19.4%, and 15%, respectively. The risk of malignancy (ROM) from the initial FNAB was estimated at 33.3%, 11.5%, 22.2%, 4.8%, 84.4%, and 96.8% for Bethesda categories I through VI, respectively. In patients with autoimmune thyroiditis (AIT), the ROM was higher than in non-AIT patients for Bethesda categories I through IV, while it was lower in category VI. The sensitivity for detecting non-benign neoplasms across Bethesda categories III through VI was approximately 86% in both AIT and non-AIT patients. However, for papillary thyroid carcinoma, sensitivity in Bethesda categories V and VI was 86% in non-AIT patients but decreased to 61.5% in AIT patients. These findings emphasize the importance of considering surgical intervention in pediatric patients with Bethesda III-VI cytology, particularly in those with AIT.