Maxillary sinus floor augmentation is frequently performed to increase bone height for dental implants, with stem cells suggested to boost bone regeneration. Consequently, this study aimed to assess the effects of incorporating stem cells in maxillary sinus floor augmentation. Two reviewers conducted an extensive search using a mix of controlled vocabulary (MeSH) and free-text terms to locate published systematic reviews. Searches were conducted in three major electronic databases (Medline via PubMed, Embase, and Cochrane database) up to July 2025. Initially, 250 articles were found, but only five studies met inclusion criteria for meta-analysis. The meta-analysis revealed a pooled standardized mean difference in new bone formation of 1.06 (95% confidence interval of −0.31 to 2.44). In a subgroup analysis comparing mesenchymal stem cells with autogenous bone, the pooled standardized mean difference was 0.88 (95% confidence interval of 0.34 to 1.42). The study’s results indicated a positive trend towards better outcomes with the use of mesenchymal stem cells, although the effect was not statistically significant at the pooled level. Additionally, combining stem cells with xenograft may yield more favorable results compared to using autogenous bone with xenograft. These findings suggest potential clinical advantages, highlighting the need for further standardized research to verify long-term outcomes.