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. Bioelectromagnetics. 35:519–530, 2014. © 2014 Wiley Periodicals, Inc.