The pathological role of human herpesviruses (HHVs) (Epstein-Barr virus [EBV], Human cytomegalovirus [CMV], and Herpes simplex virus [HSV]) in peri-implant health needs clarification quantitatively. To determine the weight of evidence for HHVs in patients with peri-implantitis (PI) and substantiate the significance of HHVs in peri-implant inflammation, electronic databases including EMBASE, MEDLINE, Cochrane Oral Health Group Trials Register, and Cochrane Central Register of Controlled Trials were searched from 1964 up to and including November 2018. Meta-analyses were conducted for prevalence of HHVs in PI and healthy controls. Forest plots were generated that recorded risk difference (RD) of outcomes and 95% confidence intervals (CI). Five clinical studies were considered and included. Four clinical studies reported data on EBV while three clinical studies reported data on CMV. Considering the risk of these viruses in PI, significant heterogeneity for CMV (χ 2 = 53.37, p < 0.0001, I 2 = 96.25%) and EBV (χ 2 = 14.14, p = 0.002, I 2 = 78.79%) prevalence was noticed between PI and healthy control sites. The overall RD for only EBV (RD = 0.20, 95% CI, 0.01-0.40, p = 0.03) was statistically significant between both groups. Frequencies of the viruses were increased in patients with PI compared with healthy nondiseased sites. However, the findings of the present study should be interpreted with caution because of significant heterogeneity and small number of included studies.