Severe pilonidal diseases have refractory symptoms despite multiple surgeries and optimal therapy remains unclear. We hypothesized that standardized minimally invasive protocol could be an effective rescue treatment. We prospectively collected data from symptomatic patients who underwent ≥ 1 pilonidal excision prior to presentation at our clinic 2019-2023. We treated these patients with standardized protocol incorporating local wound care, regular manual/laser epilation, and selective debridement/pit trephination. We treated 34 refractory patients (23 males) with median follow-up 405days. Median age of first symptoms was 17.1years; presentation to our clinic 20.0years. Prior to our clinic, 27 received one surgery (cleft lift-2, excision no closure-1, excision primary closure-18, wound vac after excision-3, excision flap closure-3); 7 had two surgeries (excision without closure + cleft lift-1, primary closure after excision twice-3, flap closure after excision twice-2, excision primary closure + excision without closure-1). We treated all patients with regular epilation ± local wound care. 14 (41%) underwent trephination ± debridement. All patients achieved complete resolution after median 52days. Five (14.7%) recurred and were treated with trephination + debridement-2 or wound care alone-3. Symptom length had no correlation with resolution time, skin type, hair amount. Standardized minimally invasive protocol requiring only selective surgical intervention can treat refractory pilonidal disease with low recurrence rate.