The findings of the prior studies investigating the resistin levels in Crohn’s disease (CD) patients and ulcerative colitis (UC) patients are inconsistent. Hence we performed the meta-analysis to systematically evaluate the serum levels of resistin in CD and UC, as well as in healthy individuals. PubMed, Web of Science, Embase, Cochrane Library and Chinese National Knowledge Infrastructure (CNKI) (as of April 30, 2020) were searched to collect all relevant published articles. We calculated the pooled standard mean difference (SMD) and 95% confidence interval (CI) by R software. Eight articles including 438 CD patients and 358 controls, and 9 articles including 391 UC patients and 438 controls were enrolled. The results showed that resistin levels were significantly elevated in patients with CD (SMD = 1.76, 95% CI: 0.64 to 2.88, p = 0.002) and UC (SMD = 2.10, 95% CI: 1.03 to 3.17, p < 0.001) compared with healthy controls. Our findings indicate that the elevated levels of serum resistin were associated with CD and UC.