Treatment of pilonidal sinus disease with conventional excision techniques is associated with recurrence up to 20 to 30% (primary closure) or with prolonged healing that might last months (closure by secondary intention). Endoscopic pilonidal sinus treatment (EPSiT) is gaining increasing popularity. This systematic review aims to summarize and evaluate the reported outcomes of pediatric EPSiT (PEPSiT) to date. Systematic search was performed for all studies on PEPSiT in patients younger than 18 years, pertaining to demographics, technique, and outcomes. Fisher's test was used to assess the associations between success/recurrence rates and different approaches (fistuloscope vs. cystoscope, different wound care protocols). A total of 320 patients (9 studies, 2018–2022) with a weighted mean age of 15.7 years and follow-up duration of 13.5 months were included. PEPSiT was successful in 290 patients (90.9%) with weighted mean time to healing of 4.1 weeks. Recurrence was reported in 29 patients (9.1%) with weighted mean time to recurrence of 4.6 months. Outcomes were not significantly altered by the use of fistuloscope versus pediatric cystoscope (p = 1.0), or with perioperative laser epilation (p = 0.06), or postoperative regular shaving, depilatory creams, light pulse, or laser (p = 0.31). The weighted mean operative time was 38 minutes and hospital stay was 16 hours. Summary of available evidence confirms that PEPSiT is safe and effective. Added to its noninvasiveness, PEPSiT's pooled outcomes appear superior to those of numerous conventional techniques. Comparison with conventional techniques, particularly off-midline flap and semi-closure procedures, is, however, lacking. The superiority of PEPSiT needs to be confirmed in future comparative studies, including cost–benefit analysis.