Magnetic fields remotely influence cellular homeostasis as a physical agent through the changes in cell physicochemical reactions. Magnetic fields affect cell fate, which may provide an important and interesting challenge in stem cell behaviors. Here, we investigated the effects of the static magnetic field (SMF, 20 mT) and electromagnetic field (EMF, 20 mT–50 Hz) on reactive oxygen species (ROS) production and the acidic pH conditions as stimuli to change cell cycle progression and cell death in mesenchymal stem cells. Results show that SMF, EMF, and their simultaneous (SMF+EMF) administration increase ROS and expression of nuclear factor erythroid 2-related factor 2 (Nrf2), superoxide dismutase 2 (SOD2), and glutathione-S-transferase (GST) as an antioxidant defense system. Besides, intracellular pH (pHi) decreases in presence of either EMF or SMF+EMF, but not SMF. Decreased ROS content using ascorbic acid in these treatments leads to increased pH compared to the magnetic field treatments alone. Furthermore, each magnetic field has different effects on the cellular process of stem cells, including cell cycle, apoptosis and necrosis. Moreover, treatment by SMF enhances the cell viability after 24 h, while EMF or SMF+EMF decreases it. These observations indicate that fluctuations of ROS generation and acid enhancement during SMF and EMF treatments may reveal their beneficial and adverse effects on the molecular and cellular mechanisms involved in the growth, death, and differentiation of stem cells.