Current evidence on selenium and its effects on cancer is conflicting. This study aimed at assessing the association between dietary intake of selenium and incidence of cancers by performing systematic review and meta-analysis of population-based prospective studies. We systematically searched for articles in Medline (Ovid), Embase, Web of Science (Thomson Reuters), China National Knowledge Infrastructure, Wanfang Database and VIP Chinese Scientific Journals. Analysis was performed in Stata version 14.2. Of the 2,564 articles obtained from the databases, 39 met our inclusion criteria, 37 were included in the final analysis. Selenium at recommended daily allowance levels of ≥55 μg/day decreased the risk of cancer [relative risk (RR) = 0.94, 95% confidence interval (CI): 0.90-0.98]. A protective effect was found in men at levels ≥55 μg/day (RR = 0.97, 95% CI: 0.94-0.99). Extra selenium intake from supplements was protective at levels ≥55 μg/day (RR = 0.89, 95% CI: 0.82-0.97). There was an inverse relationship (p value = 0.020) between selenium intake and overall cancer risk after adjusting for age, body mass index, and smoking but there was no evidence of nonlinear relationship (p value = 0.261). The findings in this study suggest that selenium is protective against cancer however the effects vary with different cancers.