The purpose of this study was to evaluate the current scientific evidence on the effectiveness of antimicrobial photodynamic therapy (aPDT) as an adjunctive treatment to mechanical debridement in the treatment of peri-implantitis. The Preferred Reporting Items for Systematic Reviews and Meta-analyses was followed. A protocol was registered in the International Prospective Registry of Systematic Reviews (PROSPERO #CRD42022361684). The search was carried out in seven databases, with no restrictions regarding language or year of publication. Our work included studies that compared clinical periodontal parameters between individuals treated with mechanical debridement associated with aPDT and a control group of patients who had undergone mechanical debridement alone. Study selection, data extraction, and risk of bias assessment (RoB 2.0) were performed by two review authors. Meta-analysis was performed. The mean difference (MD) and a 95% confidence interval (CI) were provided. Four hundred and seven-four studies were identified, of which five studies were included. The meta-analysis demonstrated that aPDT adjunctive to mechanical debridement in subjects with peri-implantitis resulted in greater reduction in probing depth 3 months after treatment than among subjects receiving treatment with mechanical debridement. Most of the included studies exhibit a low risk of bias. Adjunctive aPDT to mechanical debridement contributes to the improvement of peri-implant clinical parameters in individuals with peri-implantitis, in particular probing depth.