Abstract Background The DNA methyltransferase 3B (DNMT3B) play a significant role for methylating the intragenic regions of active genes. Findings of previous studies suggested an association between the DNMT3b 579G>T single-nucleotide polymorphism (SNP) and susceptibility to various tumors. However, limited studies have examined the association of DNMT3B 579G>T polymorphism with gastric cancer risk (GC), and their results are contradictory. This meta-analysis was carried out in order to assess this association. Methodology We conducted a thorough literature search using in PubMed, Science Direct and Google Scholar databases for relevant studies published up to January 14, 2021. A total of 5 studies were identified and included in this work. The pooled odd rates (ORs) with 95%CIs were estimated using a fixed-effect or random-effect model to take into account the heterogeneity between studies. Results We found no impact of DNMT3B 579G>T polymorphism on gastric cancer under all genetic models: Allelic model [G vs T, odds ratio (OR) = 0.79, 95% confidence of interval (CI): 0.55–1.13, p = 0.20], recessive model [GG vs GT + TT, OR = 0.96, 95% CI: 0.63–1.46, p = 0.86], dominant model [GG + GT vs TT, OR = 0.72, 95% CI: 0.47–1.10, p = 0.13], heterozygous model [GT vs TT, OR = 0.70, 95% CI: 0.45–1.08, p = 0.11] and homozygous model [GT vs TT, OR = 0.72, 95% CI: 0.44–1.17, p = 0.18], homozygous, OR: 0.72, 95% CI = 0.44–1.17, p = 0.18). Conclusion Our results indicated that DNMT3B 579G>T is not associated with GC, and it may not be used as a stratification marker to predict susceptibility.