Objective B cell activating factor (BAFF) is a key regulator of Primary Sjögren’s Syndrome (pSS), which is characterized by B lymphocyte hyperactivity. BAFF is also known as TNF ligand superfamily member 13B (TNFSF13B). This study aimed to explore whether five single nucleotide polymorphisms (SNPs) of the TNFSF13B gene (rs9514827, rs1041569, rs9514828, rs1224141, and rs12583006) are related to pSS susceptibility. Methods We searched Pubmed, Cochrane, Elsevier, Web of Science, CNKI, CQVIP, and WanFang databases (up to January 2023). In a population with pSS, the odds ratios (ORs) with 95% confidence intervals (CIs) of genotypes and each allele were provided to investigate relationships between the polymorphisms of the BAFF (TNFSF13B) gene and pSS. Results The meta-analysis in question contains three studies. In the group of pSS patients and randomly selected health controls (HCs), there was a statistically significant relationship between rs1041569 and rs12583006 and pSS susceptibility, respectively. In fixed models, there were statistical differences in pSS patients and randomly chosen HCs. Conclusions There were relationships of rs1041569 and rs12583006 in the pSS group and HC group. BAFF(TNFSF13B) genes, particularly rs1041569 and rs12583006, were related to pSS susceptibility in pSS patients.