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Abstract Background Pilonidal disease ( PD ) is a common inflammatory disease of the gluteal fold, resulting in recurrent acute/chronic infection at the level of the natal cleft. In this study, endoscopic pilonidal sinus treatment ( EPS iT), a new endoscopic minimally invasive procedure, was evaluated for its effectiveness in treating PD . Methods Two hundred and fifty prospective patients with chronic PD were enrolled in a prospective multicentre study conducted at a secondary and tertiary colorectal surgery centre. The primary end‐point of this study was wound healing, and the short‐/long‐term outcomes such as healing time, morbidity rate and recurrence rate were analysed. The secondary end‐point of this study was quality of life (QoL). Results The complete wound healing rate was 94.8%, and the mean complete wound healing time was 26.7 ± 10.4 days. The incomplete healing rate (5.2%) was significantly related to the number of external openings ( P = 0.01). There was no difference in the failure rate when EPS iT was performed as the first‐line treatment for PD or when it was used after unsuccessful procedures ( P = n.s.). Recurrence occurred in 12 cases (5%). The QoL significantly increased from preoperative levels 15 days after the EPS iT procedure (45.3 vs 7.9; P < 0.0001). Conclusions The EPS iT procedure is a safe and effective technique for treating PD . It provides better short‐ and long‐term outcomes than various other techniques that are more invasive. EPS iT is a minimally invasive outpatient procedure, which is associated with a quick recovery and a good QoL outcome.