Magnetic hyperthermia using magnetic nanoparticles (MNPs) draws significant interest for application in heat therapy for cancerous tumors, wherein it is important to improve the heating efficiency, i.e., increase the hysteresis loss. In the present study, we examined the hysteresis loss of magnetically fractionated MNPs for hyperthermia application. Original Resovist MNPs were magnetically fractionated into three types, and their hysteresis loops were measured with an excitation field of 2.5 mT (rms) at a frequency of 20 kHz. The hysteresis loss of the fractionated MNPs with the larger magnetic moment was approximately two times that of the original Resovist MNPs. A numerical simulation based on the Langevin function was performed to support the experimental results. From the experimental and simulation results, we can conclude that the efficiency of hyperthermia is improved by magnetically separating MNPs.