Mesenchymal stem cells (MSCs) offer great potential for use in stem cell-based therapies due to their unique regenerative potential via reconstructive and paracrine capacities. These therapies offer new hope for patients suffering from conditions that have no cure. Currently, mesenchymal stem cells (from adipose tissues, bone marrow, and umbilical cords) are most interesting for application in those therapies. Nevertheless, the development of MSC-based medical products requires thorough research and standardization that maximizes the therapeutic effect while minimizing side effects. One of the interesting novel approaches to achieving this goal is combining MSC therapy with an electromagnetic field (EMF). Many studies have shown that EMF can enhance the regenerative properties of MSCs by influencing stem cell fate through modulating differentiation, proliferation, cell cycle regulation, metabolism, and cytokine and growth factor secretions. Combination therapy of EMF-MSCs is a promising perspective; however, it is important to select appropriate EMF parameters to obtain beneficial therapeutic effects. Therefore, understanding the mechanisms involved in the EMF impact on MSCs is crucial. In this study, we provide an overview of the effects of EMF on the biological response and “fate” of MSCs, paying attention to the gaps in research that remain unfilled and discuss the clinical application of this approach.