Aim Pediatric endoscopic pilonidal sinus treatment (PEPSiT) has favorable short-term-outcomes, but there is a lack of reliable data on medium and long-term follow-up. The objective of our study was to evaluate the effectiveness and advantages of PEPSiT versus conventional surgery of pilonidal sinus in the pediatric population. Methods A quasi-experimental study was carried out in pediatric patients undergoing pilonidal sinus surgery at a single institution from 2019 to 2022. Excision and healing by secondary intention (EHSI), excision and primary closure (EPC), and PEPSiT were compared. The surgical technique chosen was surgeon-dependent. Results In total, 149 patients were studied-100 undergoing PEPSiT, 28 undergoing EHSI, and 21 undergoing EPC. Median full healing process was 4 weeks [interquartile range (IQR): 3-8] in PEPSiT, 16 weeks in EHSI (IQR: 12-26.5), and 7 weeks (IQR: 4-10) in ECP (p < 0.01). Pain on the visual analogue scale (VAS) and need for analgesics were lower in the PEPSiT group (p < 0.01). Mean time to return to normal life was shorter with PEPSiT-177 days earlier than EHSI (95% CI 124.7-230.2; p < 0,01) and 7.2 days earlier tan EPC (95% CI 20.2-138.6; p < 0,009). Complications with PEPSiT were 9.3 times lower tan EHSI [odds ratio (OR) 9.3; 95% confidence interval (CI) 3.5-24.7] and 8.5 times lower than ECP (OR = 8.5; 95% CI 2.9-24.4). EHSI had 5.3 times more probability of recurrence than PEPSiT (OR = 5.3; 95% CI 1.3-22.7), and ECP 15.2 times more (OR = 15.2; 95% CI 3.2-71.7). Conclusions Endoscopic pilonidal sinus treatment is effective in medium-term follow-up, with fewer complications than classic techniques. It allows for an early return to normal life without restrictions.