Background Treatment of palmar and axillary primary focal hyperhidrosis (PFH) in children up to 16 years using thoracoscopic sympathicotomy is supported by scarce evidence. Therefore, this study aimed to summarize the results of our standardized bilateral, one-stage, single-port sympathicotomy (BOSS) in children up to 16 years of age. Methods Consecutive children (n = 14) up to 16 years of age undergoing BOSS between October 2011 and June 2015 in our institution were included in this retrospective study. Results Recurrence of primary hyperhidrosis was noted in seven patients (50.0%), of whom five patients (35.7%) underwent reoperation. Reoperations were associated with placement of additional thoracoscopic ports (n = 1; 12.5%), intraoperative placement of pleural drains (n = 2; 25%), and prolonged air leak (n = 1; 12.5%). Despite the high recurrence and reoperation rates, overall patient satisfaction was high with a median satisfaction score of 7.5 (interquartile range of 1.75; range: 4-9). Conclusion Although the overall patient satisfaction score in our cohort was good, BOSS for the treatment of intolerable palmar and axillary PFH in children up to 16 years of age is associated with a high recurrence and reoperation rate.