Neurological diseases, including ischemic stroke, are considered a big challenge for public health due to their high prevalence and lack of definitive and effective treatments. Addressing these issues requires innovative therapeutic approaches and among the limited methods available, stem cells have shown promise in improving central nervous system repair by enhancing myelin regeneration and neuronal recovery. To advance this field of research, this systematic review aims to assess the safety and effectiveness of mesenchymal stem cells (MSCs) derived from both bone marrow and adipose tissue for the treatment of ischemic stroke. This study conducted a systematic review in the electronic databases PubMed, Scopus, Web of Science, Embase, ScienceDirect, and Google Scholar to assess the efficacy and safety of MSCs generated from bone marrow and adipose tissue for the treatment of ischemic stroke. It was extracted without a time limit until April 2023. The studies were then transferred to the information management program (EndNote) and duplicates were eliminated. The remaining studies were then examined using the entry and exit criteria and the 3 stages of primary, secondary, and qualitative evaluation, and finally, the results of the final studies were extracted. According to the initial search in the desired databases, 1028 possible related articles were identified and transferred to the information management software (EndNote). After removing 390 duplicate studies, 608 studies were excluded based on inclusion and exclusion criteria. Finally, 37 final studies were included in the systematic review process. Based on the investigations, it was evident that the administration of MSCs derived from both bone marrow and adipose tissue holds significant promise as an effective and safe treatment approach for ischemic stroke. The results consistently showed acceptable outcomes in the studies and this evidence can be recommended for the clinical application of this treatment. Also, the findings of this study report that the use of adipose tissue and bone marrow MSCs in the treatment of ischemic stroke can be used as a practical method.