Objective To investigate the clinical characteristics, therapeutic methods, and prognostic factors of patients with rectal stromal tumor. Methods The clinicopathological data of 33 patients with rectal stromal tumor who treated in the Affiliated Hospital of Xuzhou Medical University from January 2008 to November 2014 were retrospectively reviewed, and the therapeutic methods and prognostic factors of these patients were further analyzed. Results The major clinical manifestations of 33 patients included abdominal discomfort in 21 patients, changes of defecation habit and fecal property in 15 patients, bloody stool in 13 patients, and anal pain in 9 patients. CT and MRI examination showed a mass in the pelvic with the clear boundary, growed through the wall of rectum, with the heterogeneous density and signal, sometimes with necrosis, calcification, and haemorrhage. The results of immunohistochemical staining showed that, 31 patients were strongly positive for CD117, 28 patients were strongly positive for CD34, 15 patients were positive for smooth muscle actin (SMA), 13 patients were positive for vimentin, and 3 patients were positive for soluble acid protein (S-100). The therapeutic methods of 33 patients included local excision in 13 patients, low anterior resection in 11 patients, abdominal pelvic resection in 5 patients, and conservative treatment in 4 patients. A total of 26 patients underwent surgery combiend with imatinib therapy. The follow-up time was 10–102 months and the median time was 58 months. During follow-up period, there were 8 patients suffered from recurrence or metastasis, and 15 patients died. The results of Cox proportional hazards regression model showed that, postoperative relapse and metastasis were prognostic factors for survival〔RR=19.338, 95% CI was (2.821, 132.568), P=0.003〕. The survival situation of the patients suffered from postoperative relapse and metastasis was poor. Conclusions CD117 and CD34 could serve as valuable diagnostic indexes for rectal stromal tumor. Surgery is an effective treatment for rectal stromal tumor.