Background Over the past few decades, surgery for Hirschsprung’s disease (HD) has evolved into a minimally invasive, single-stage procedure with excellent outcomes. Intraoperative frozen section biopsy is critical for this procedure to avoid the potential risk of leaving a retained aganglionic segment. However, this facility is not available in most low-income countries. Therefore, a two-stage procedure with an initial colostomy is still practiced in the developing world. We aimed to evaluate the outcome of single-stage transanal pullthrough performed in a facility without frozen section biopsy. Methods A retrospective review of all patients who underwent transanal pullthrough in two teaching hospitals over a 6-year period (2015–2020). Results Forty-seven children underwent transanal endorectal pullthrough (TERPT). Age at surgery ranged from 2 months to 6 years and mean weight was 8.7 kg. Barium enema did not show transition zone in 6 patients (12.8%) while others demonstrated short segment HD. Intraoperatively, the transition zone was visualized in 40 patients (85%). TERPT alone was performed in 35 (74.5%), TERPT with laparotomy to visualize transition zone in 9 (26.7%) and TERPT with transabdominal mobilization was required in 3 (6.4%). Definitive histopathologic examination revealed aganglionic segment pullthrough in 4 (8.5%) and transitional zone pullthrough in another 4 (8.5%). However, with long term follow up all eight children remained asymptomatic and no intervention was required. Conclusions Transanal pullthrough offers reduced number of surgeries and faster recovery. We have also observed a good functional outcome despite a discrepancy with pathology results. Overall, our data suggests it is a safe and viable option for the treatment of short segment HD in facilities where frozen section is not available.