To evaluate the incidence, management, and outcomes of rectal injury (RI) and subsequent rectovaginal fistula (RVF) during gender-affirming vaginoplasty (GAV) at a high-volume transgender surgery center. We performed a retrospective review of preoperative, intraoperative and post-operative findings of all patients with RI during GAV from January 2016 to September 2022. Descriptive statistics were calculated using Microsoft Excel. RI occurred in 9 of 1011 primary GAV and colorectal surgery (CRS) consulted in 5 cases, which included sigmoidoscopy with an air leak test in 4 and with temporary bowel diversion in 2. Of the 9, 6 proceeded with full-depth GAV, and 3 were converted to minimal-depth vaginoplasty. Two had bulbospongiosus muscle interposition and none had a concomitant urethral injury. 1/9 patients with RI developed a RVF which occurred in a patient with prior perineal surgery and no intraoperative sigmoidoscopy. Three (50%) with full-depth GAV developed vaginal stenosis postoperatively. RI during primary GAS in experienced hands is uncommon with an incidence of 0.89% in our series of 1011. Unusual tissue dissection planes were a risk factor. If injuries were identified intraoperatively, repaired with multilayer closure and evaluated by CRS, patients did well without the development of RVF despite completion of full-depth GAV. It is reasonable to complete the full-depth vagina, but patients should be advised of a significant risk of post-operative vaginal stenosis.