Due to limited information reported on the clinical characteristics and outcomes of Burkitt lymphoma (BL) patients with gastrointestinal (GI) involvement, here we used the Surveillance, Epidemiology, and End Results (SEER) database to perform our study in a population-based scale. Extranodal GI involvement was categorized into gastric and intestinal primary sites. A total of 477 BL patients with GI involvement extracted from the SEER database between 2004 and 2015 were included in this study, 112 (23.5%) with the stomach and 365 (76.5%) with the intestine. Our study demonstrated that gastric involvement, older age, male gender, black race, advanced-stage III/IV, no-chemotherapy, and earlier years of diagnosis were associated with a significantly worse overall survival (OS) in GI BL patients after adjustment in multivariate analysis, whereas marital status did not significantly influence OS. Notably, BL Patients with gastric involvement had a significantly inferior 5-year OS in both univariate and multivariate analysis, as compared to those with intestinal involvement (37.8% vs. 70.2%; Univariate: HR = 2.637, P < .001; Multivariate: HR = 1.489, P = .016). In subgroup analysis, we demonstrated that gastric BL patients had a consistently worse OS than intestinal patients regardless of gender, clinical stage and year of diagnosis. Hopefully, with the advances in modern therapy, improved survival has been found in BL patients with GI involvement as a whole, specifically those with gastric involvement (HR = 0.529, P = .011) in recent years of diagnosis. In conclusion, despite the improved survival achieved in recent years, the prognosis of BL patients with gastric involvement is still poor. Novel personalized therapies and better access to intensive care remain to be needed.© 2020 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.