Purpose: We assessed the effect of performing colpectomy before (primary) or after (secondary) gender affirming surgery with single stage urethral lengthening on the incidence of urethral fistula in transgender men. Materials and Methods: We retrospectively reviewed the charts of all transgender men who underwent gender affirming surgery with urethral lengthening between January 1989 and November 2016 at VU University Medical Center. Patient demographics, surgical characteristics, fistulas and fistula management, and primary and secondary colpectomy were recorded. Descriptive statistics were calculated and incidence rates were compared. Results: A total of 294 transgender men underwent gender affirming surgery with urethral lengthening. A urethral fistula developed in 111 of the 232 patients (48%) without colpectomy and in 13 of the 62 (21%) who underwent primary colpectomy (p <0.01). Secondary colpectomy resulted in 100% fistula closure when performed in 17 patients with recurrent urethral fistula at the proximal urethral anastomosis and the fixed part of the neourethra. Conclusions: Primary colpectomy decreases the incidence rate of urethral fistulas. Secondary colpectomy is also an effective treatment of fistulas at the proximal urethral anastomosis and the fixed part of the neourethra.