In this paper, we present a new method for targeted hyperthermia using an electromagnetic navigation system. Typically, Fe₃O₄ magnetic nanoparticles (MNPs) are utilized by injection methods. However, the study demonstrated that the proposed method provides active locomotion for targeting a destination within a three-axis Helmholtz coil, and generates heat through a high-frequency heating coil. To realize these two functions, the entire system combined the electromagnetic navigation system and a high-frequency heating system. The Fe₃O₄ MNPs were prepared via chemical synthesis. Using vibrating sample magnetometer (VSM) and X-ray diffraction (XRD), we observed the magnetic properties and structure of the crystals. Through various experimental tests, we investigated the controllability, mobility, and steering ability of the MNPs. In particular, we confirmed the heating characteristics of the fabricated MNPs according to the changes in the magnetic field strength at 205 kHz. On average, the particle cluster generated a temperature of 73.12 °C at 58 kA/m.