It was reported that obese (Ob/Ob) mice lose their weight and fat when treated with 0.5 T direct current electromagnetic fields. We also observed that 7.5 Hz, 0.4 T rotation of extremely low frequency magnetic fields (ELF-MF) has an inhibitory effect on obesity. Mesenchymal stem cells (MSCs) are multi-potent cells capable of differentiating to different MSC lineages, including adipose. We hypothesized that inhibitory effects of ELF-MF on obesity may be related to the differentiation of MSCs to adipocytes. In the present study, we investigated the effects of 7.5 Hz, 0.4 T ELF-MF on differentiation of human umbilical cord MSCs. We found that ELF-MF inhibited adipogenic differentiation (exposed 2 h/day for 15 days) of MSCs but had no effect on osteogenic differentiation (exposed 2 h/day for 21 days). Moreover, ELF-MF inhibited adipocyte-specific expression of peroxisome proliferator-activated receptor 2 (PPARγ2). ELF-MF promoted c-Jun N-terminal kinase (JNK)-dependent intracellular signaling in MSCs. Furthermore, activation of the non-canonical Wnt pathway provoked the inhibition of PPARγ2 expression resulting in suppression of adipogenic differentiation. In addition, the effects of ELF-MF on growth and apoptosis of MSCs were not observed. Our data indicated that ELF-MF of 7.5 Hz, 0.4 T inhibited the adipogenic differentiation of MSCs via JNK-dependent Wnt signaling pathway, but had no effect on the growth and function of MSCs, suggesting the inhibitory effect of ELF-MF on obesity may be attributed to the inhibition of differentiation of MSCs into adipocytes. This study may provide a potential approach for the treatment of obesity.