An innovative electroslag remelting furnace with a water-cooled electrode was introduced to recycle the rejected electrolytic manganese metal (EMM) scrap. To clarify the desulfurization process in the rejected EMM scrap, a transient three-dimensional comprehensive numerical model was elaborated. Using the magnetic potential vector approach, the respective electromagnetic fields were calculated via the Maxwell equations. The Lorentz force and the Joule heating fields were derived as phase distribution functions and interrelated via the momentum and energy conservation equations as source terms, respectively. The molten manganese metal droplet motion, as well as the fluctuation of the slag–metal interface, was described by the volume-of-fluid (VOF) approach. Besides, the solidification was modeled via the enthalpy-based technique. A thermodynamic module was established to estimate the sulfur mass transfer rate between the molten manganese metal and the molten slag. Furthermore, a factor related to the magnitude and frequency of the alternating current and the physical properties of the melt was introduced to include the electro-emulsification phenomenon. An experiment has been carried out with a commercial-scale ESR device. The predicted values of the slag temperature and sulfur content in the final manganese ingot were found to agree reasonably with the corresponding measured data. Under continuous melting of the rejected EMM scrap, molten manganese metal droplets are formed at the domain inlet, grow, and fall down. Highly conductive molten manganese metal droplets significantly change distributions of the current streamline, the Joule heating, and the Lorentz force around and within it. Moreover, droplets are inclined to rotate and move inside the mold. With the renewal of the slag–manganese interface, sulfur in the molten manganese metal is constantly transferred to the molten slag. With the applied current ranging from 3000 to 4000 A, the average sulfur content of the manganese ingot dropped from 0.0447 to 0.0291 pct, and thus, the desulfurization rate rose from 55.3 to 70.9 pct.