This systematic review considers the evidence from animal studies evaluating the effectiveness of mesenchymal stem cells (MSC) in the treatment of intraoral peri‐implant defects. MEDLINE, EMBASE, and LILACS databases were searched for quantitative preclinical controlled animal model studies that evaluated the effect of MSC on bone healing at intraoral peri‐implant bone defects. The primary outcome was the amount of (re‐)osseointegration reported as bone‐to‐implant contact in the defect area. The systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses statement guidelines. Ten studies met the inclusion criteria. Only one study induced peri‐implant inflammation to produce peri‐implant bone defects. In all others, defects were surgically created at implant installation. Differences in defect morphology were identified among the studies. Both xenogenous and autogenous MSC were used to treat peri‐implant defects. These included bone marrow‐derived MSC, periodontal ligament‐derived MSC, umbilical cord MSC, bone marrow‐derived mononuclear cells, and peripheral blood mononuclear cells. Meta‐analysis was not possible because of heterogeneities in study designs. Nonetheless, in most studies, local MSC implantation was not associated with adverse effects and had a positive effect on bone healing around peri‐implant defects. Combination of MSC with membranes and bioactive factors appears to provide improved treatment outcomes. In large animal models, intraoral use of MSC may provide beneficial effects on bone healing within peri‐implant defects. The various degrees of success of MSC in peri‐implant bone healing are likely to be related to the use of cells from various populations, tissues, and donor species. However, human safety and efficacy must be demonstrated before its clinical use can be considered.