Abstract Background and objectives The best surgical approach to rectal gastrointestinal stromal tumors (GISTs) is still debated, and both nonanatomic rectal resection (NARR) and anatomic rectal resection (ARR) are applied. The aim of this study was to evaluate the feasibility and oncological outcomes of NARR and ARR for rectal GISTs (R‐GISTs). Methods Through a large French multicentre retrospective study, 35 patients were treated for R‐GIST between 2001 and 2013. Patients who underwent NARR and ARR were compared. Results There were 23 (65.7%) patients in group ARR and 12 (34.3%) in group NARR. Significantly more patients in the group with ARR had a neoadjuvant treatment (86%) with tyrosine kinase inhibitor (TKI) (imatinib) compared to those with NARR (25%) ( p < .01). The median preoperative tumor size was significantly different between the groups without and with neoadjuvant TKI: 30 ± 23 mm versus 64 ± 44.4 mm, respectively ( p < .001). Overall postoperative morbidity was 20% ( n = 7) (26% for ARR vs. 8% for NARR; p = .4). After a median follow‐up of 60.2 (3.2–164.3) months, the 5‐year disease‐free survival rates were 79.5% (confidence interval [CI] 95%: 54–100) for the NARR group and 68% (CI 95%: 46.4–89.7) for the ARR group ( p = .697), respectively. Conclusion The use of NARR for small R‐GIST's does not seem to impair the oncological prognosis.