(1) Background: The aim of the study was to evaluate the benefit of combining chlorhexidine with the mechanical treatment of peri-implant mucositis. (2) Methods: Articles from 2016 to 2021 included in the PubMed and Scopus databases were analyzed, following the PICOS criteria and the randomized controlled study model that used chlorhexidine in various forms in the treatment of peri-mucositis. According to the established criteria, a limited number of studies were selected. These studies had as their criteria of evaluation for the effectiveness of chlorhexidine, plaque indices, bleeding indices and depth probing indices. Chlorhexidine has been used after mechanical debridement as a solution, with different concentrations of 0.06%/0.12%/0.2% alone or in a concentration of 0.03%, in combination with 0.05% cetylpyridinium chloride, as well as in the form of a gel with a concentration of 0.2%. (3) Results: The results were assessed to a placebo or other substances, and showed a significant reduction in the indices with a follow-up period ranging from 3 months to 1 year. (4) Conclusions: The association of chlorhexidine with the mechanical treatment of peri-implant mucositis has a role in reducing inflammation, although a complete remission was not obtained in all cases, and the results were not statistically significantly different from the use of other antiseptics.