Numerous studies have investigated association between the germline HOXB13 p.Gly84Glu mutation and cancer risk. However, the results were inconsistent. Herein, we performed this meta-analysis to get a precise conclusion of the associations. A comprehensive literature search was conducted through Medline (mainly Pubmed), Embase, Cochrane Library databases. Crude odds ratios (ORs) and their 95% confidence intervals (CIs) were calculated by STATA 12.1 software to evaluate the association of HOXB13 p.Gly84Glu mutation and cancer susceptibility. Then, 25 studies including 51,390 cases and 93,867 controls were included, and there was significant association between HOXB13 p.Gly84Glu mutation and overall cancer risk (OR = 2.872, 95% CI = 2.121–3.888, P < 0.001), particularly in prostate cancer (OR = 3.248, 95% CI = 2.313–4.560, P < 0.001), while no association was found in breast (OR = 1.424, 95% CI = 0.776–2.613, P = 0.253) and colorectal cancers (OR = 2.070, 95% CI = 0.485–8.841, P = 0.326). When we stratified analysis by ethnicity, significant association was found in Caucasians (OR = 2.673, 95%CI = 1.920–3.720, P < 0.001). Further well-designed with large samples and other various cancers should be performed to validate our results.