BACKGROUND: This study aimed to compare the outcomes of a modified submucosal ligation of the fistula tract (MSLOFT) technique with the hybrid seton technique for treating transsphincteric anal fistulas. MATERIAL AND METHODS: A retrospective analysis was conducted with ethical approval from Baskent University. Patients over 18 years of age with a diagnosis of transsphincteric fistula and complete data were included in the study. Patients with fistulas of non-cryptoglandular origin, incontinence, multiple fistula tracts, inflammatory bowel disease, or malignancy were excluded. The study involved 255 patients, divided into: MSLOFT (n = 31) and hybrid seton (n = 224) groups. Propensity score matching (PSM) was performed to balance age, gender, and body mass index between the groups, resulting in 30 patients per group. RESULTS: There was no significant difference between the MSLOFT and hybrid seton groups regarding Wexner scores, incontinence rates, recurrence, or reoperation rates, in the overall cohort and after PSM. However, in the overall cohort and after PSM analysis, the operation time ( CONCLUSION: MSLOFT is a feasible and effective sphincter-preserving technique for transsphincteric anal fistulas, providing low recurrence and incontinence rates similar to the hybrid seton technique.