The present study focuses on the development of a methodology for evaluating the safety of MNH systems, through the numerical prediction of the induced temperature rise in superficial skin layers due to eddy currents heating under an alternating magnetic field (AMF). The methodology is supported and validated through experimental measurements of the AMF’s distribution, as well as temperature data from the torsos of six patients who participated in a clinical trial study. The simulations involved a computational model of the actual coil, a computational model of the cooling system used for the cooling of the patients during treatment, and a detailed human anatomical model from the Virtual Population family. The numerical predictions exhibit strong agreement with the experimental measurements, and the deviations are below the estimated combined uncertainties, confirming the accuracy of computational modeling. This study highlights the crucial role of simulations for translational medicine and paves the way for personalized treatment planning.