The optimal management of pilonidal disease in the pediatric population is still debated. We conducted a retrospective review of patients 21 years old and younger who underwent surgical management for pilonidal disease between 2009 and 2013 at a single pediatric institution. Sixty patients (41.7% male) were included in the analysis, with a mean age of 15.0 years (range, 13-20). Twelve (20%) had a prior drainage procedure for pilonidal abscess before the definitive operative treatment. After excision to the presacral fascia, 36 (60%) had primary closure, 17 (28.3%) were left to heal by secondary intention, and 7 (11.7%) had flap closure. Overall recurrence rate was 41.7 per cent with 33.3 per cent in the primary, 58.8 per cent in the secondary, and 42.9 per cent in the flap group, respectively. Ten (16.7%) patients developed postoperative complications, which were similar among surgical groups, gender, and body mass index. The average length of stay was 0.67 (median 0, range, 0-5) days. Primary closure had the shortest length of stay (analysis of variance P = 0.04), and flap closure had no reoperations (analysis of variance P < 0.01). Pilonidal disease remains surgically challenging. Our data suggest that excision and primary closure is a better option in the pediatric population.