The underlying causes of failure or recurrence after ligation of the intersphincteric fistula tract are postulated to be refistulization, breakdown of the closure wound in the intersphincteric plane and faecal contents entering the internal opening, thereby causing recurrent infection. The aim of this study is to demonstrate the outcomes of subtotal fistulectomy with sliding anoderm flaps to prevent refistulization. This retrospective study used prospectively collected data. Patients with transsphincteric or intersphincteric fistulas were enrolled between August 2021 and July 2023. An anal manometric study was performed before and after surgery. Faecal incontinence was evaluated using the faecal incontinence severity index (FISI). Failure was defined as nonhealing of the surgical wound or fistula. Fifty-one patients who underwent subtotal fistulectomy with a sliding anoderm flap were included. After a median follow-up of 12 months (range 4-27 months), primary healing was achieved in 49 patients (96%). Two patients experienced treatment failure, while none developed postoperative recurrence. The median healing time was 10 weeks (range 6-24 weeks). The FISI scores did not change significantly after the surgery. The median resting pressure significantly reduced after surgery [125 cmH2O (range 59-204 cmH2O) vs. 99 cmH2O (range 36-176 cmH2O); p = 0.0001]. The median squeeze pressure significantly decreased after surgery [356 cmH2O (range 137-579 cmH2O) vs. 329 cmH2O (range 72-594 cmH2O; p = 0.005)]. Subtotal fistulectomy with a sliding anoderm flap showed excellent healing rates with no postoperative deterioration of anal function.