Treating diseases such as Muscular dystrophy (MD) and HIV/AIDS poses several challenges to the rapidly evolving field of regenerative medicine. Previously, stem cell therapy has been said to affect the clinical courses of HIV/AIDS and MD, but, in practice, eradication or control of these diseases was not achievable. The introduction of gene editing into stem cell therapy has stimulated HIV/AIDS and MD cell therapy research studies substantially. Here, we review current methods of treating HIV/AIDS and MD using stem cell therapy. This review also details the use of different types of cells and methods in cell therapy and the modeling of new cell-based therapies to treat Duchenne muscular dystrophy. We speculate that the effective use stem cell therapy in conjunction with other treatment therapies such as steroids and rehabilitation could improve livelihood.