In this paper we present an experimental set up for long-term irradiation of cells with high-power terahertz pulses with intensities of about 23 GW/cm2. The system was shown to be a reliable tool for cell irradiation in single-point irradiation mode as well as in scanning mode. Wharton’s Jelly derived mesenchymal stem cells were exposed to high power THz pulses with a field strength of about 3 MV/cm for 90 min for the first time. Preliminary results on THz radiation effects on cell viability and proliferation were obtained.