Background: The impact of gastrointestinal endoscopy on COVID-19 infection remains poorly investigated. We herein performed a systematic review and meta-analysis to evaluate the outcomes of COVID-19 in patients undergoing gastrointestinal endoscopy. Method: Ovid Medline, Ovid EMBASE, Ovid the Cochrane Library, and other electronic databases were searched until 30 November 2020 to identify publications with confirmed COVID-19 infection in patients undergoing gastrointestinal endoscopy. The primary outcomes were SARS-CoV-2 transmission, personal protective equipment use, rates of case fatality, complications, and procedural success. Results: A total of 18 articles involving 329 patients were included in this systematic review and meta-analysis. The overall basic reproduction rate is 0.37, while the subgroup results from Asia, Europe, and North America are 0.13, 0.44, and 0.33, respectively. The differences in personal protective equipment use between the positive transmission and non-transmission group are mainly in isolation gowns, N95 or equivalent masks, and goggles or face-shields. The rate of case fatality, complication, and procedural success are 0.17 (95% confidence interval = 0.02–0.38), 0.00 (95% confidence interval = 0.00–0.02), and 0.89 (95% confidence interval = 0.50–1.00), respectively. The fatality rate in Europe was the highest (0.23, 95% confidence interval = 0.04–0.50), which is significantly different from other continents ( p = 0.034). Conclusion: The risk of SARS-CoV-2 transmission within gastrointestinal endoscopy units is considerably low if proper use of personal protective equipment is applied. Similarly, a low fatality and complication rate, as well as a high procedural success rate, indicated that a full recovery of endoscopic units should be considered.