The effect of nanosecond electromagnetic pulses on human health, and especially on forming free radicals in human cells, is the subject of continuous research and ongoing discussion. This work presents a preliminary study on the effect of a single high-energy electromagnetic pulse on morphology, viability, and free radical generation in human mesenchymal stem cells (hMSC). The cells were exposed to a single electromagnetic pulse with an electric field magnitude of ~1 MV/m and a pulse duration of ~120 ns generated from a 600 kV Marx generator. The cell viability and morphology at 2 h and 24 h after exposure were examined using confocal fluorescent microscopy and scanning electron microscopy (SEM), respectively. The number of free radicals was investigated with electron paramagnetic resonance (EPR). The microscopic observations and EPR measurements showed that the exposure to the high-energy electromagnetic pulse influenced neither the number of free radicals generated nor the morphology of hMSC in vitro compared to control samples.