Background and Objectives: The rarity of duodenal gastrointestinal stromal tumors (DGIST) led to only limited data being available on their management and prognosis. We retrospectively analyzed the clinicopathological features, surgical treatments, adjuvant therapy, and prognosis of DGIST. Methods: Sixty-one patients were identified at diagnosis of primary DGIST from February 2005 to December 2015. One hundred twenty six patients with small intestinal gastrointestinal stromal tutors (GIST) were selected as control groups. Survival analyses were calculated using the Kaplan-Meier method. Results: Three- and five-year recurrence/metastasis-free survival rates of patients with DGIST were similar to those of patients with small intestinal GIST (p > 0.05 for all). Out of 61 cases with DGIST, 45 patients were treated with Limited Resection (LR). Sixteen patients were treated with Pancreaticoduodenectomy (PD). The 3- and 5-year recurrence/metastasis-free survival rates of the PD group and LR group were of no significant difference (p > 0.05 for all). Univariate analysis indicated that factors including surgical approaches, mitotic count, size, and risk grades were significantly associated with recurrence/metastasis-free survival (log-rank test, p < 0.05). Multivariate analysis demonstrated that the mitotic count was independently correlated with a worse recurrence/metastasis-free survival. Conclusions: Patients with radical resected DGIST had a favourable prognosis, which is similar to that of small intestinal GIST. Both LR and PD were optimal choices for treating DGIST.