Rectal gastrointestinal stromal tumors (GISTs) are rare, and limited information is available concerning their management and long-term outcomes. We retrospectively evaluated the clinicopathological characteristics, surgical management, and long-term outcomes of rectal GISTs from a single institution.All surgically treated patients with rectal GISTS at the Department of General Surgery, West China Hospital, Sichuan University were identified between January 2005 and May 2014. The overall survival (OS) and disease-free survival (DFS) were assessed by the Kaplan-Meier method.Forty-five patients with rectal GISTs (33 males and 12 females) were identified. Patients presented with rectal bleeding (n = 13; 28.9%) and altered bowel habits (n = 11; 24.4%). The cohort study of 45 patients included 4 very low-risk, 10 lowrisk, 1 intermediate-risk, and 30 high-risk patients. A total of 21, 13, and 11 patients underwent local resection (Group 1), abdominoperineal resection (Group 2), and super-low or low anterior resection (Group 3), respectively. Group 1 had a smaller tumor sizes and shorter distances from the anal verge compared with the other groups (P < 0.05). The one-, three-, and fiveyear DFS rates for the entire cohort study were 90.4%, 69.3%, and 57.0%, respectively. High National Institutes of Health (NIH) risk categories (HR = 1.62) were associated with low DFS rates (P = 0.035). The DFS was significantly improved by imatinib mesylate (IM) adjuvant therapy in the high-risk subgroup (P = 0.001).The type of surgery should be chosen based on the location and size of the rectal GISTs. Adjuvant IM therapy was associated with improved DFS in patients with high-risk tumors, and classification was strongly associated with the patient outcome.