To explore the effect of selective serotonin re-uptake inhibitors (SSRIs) on risk of type II diabetes mellitus (T2DM) and acute pancreatitis (AP), expecting to provide guidance for clinic. Literature was retrieved by searching Pubmed, Embase, Cochrane and Scopus and hand searching of reference lists of related articles. Stata 14.0 was utilized for processing and analysis, and adjusted odds ratios (aORs) were applied. Our study included 113898 T2DM patients and 284131 controls from nine studies and 17548 AP patients and 108108 controls from four studies. The pooled aORs of SSRIs on the risk of T2DM and AP were 1.38 (95% confidence interval (CI) = 1.24–1.54) and 1.26 (95% CI = 1.13–1.40), respectively. Study design, quality, ethnicity, follow-up, and sample size of patients were the resources of heterogeneity. Subgroup analysis showed that 2 weeks is a high-risk time for AP after SSRIs use, with 1.48-fold-times as much after it. This meta-analysis provides evidence of a significant positive association between SSRIs use and risks of T2DM or AP, and duration of 2 weeks of SSRIs use has higher risk of AP, which should be paid much attention to.