A beam direct energy converter (BDC) is designed to recover unneutralized ion beam energies in a 500-keV negative-ion-based deuterium neutral beam injection system for the Fusion Experimental Reactor of Japan Atomic Energy Research Institute. A newly developed three-dimensional beam transport code KUNABE-3 is used. Due to approximately equal fractions of unneutralized D+ and D− beams flowing from the gas neutralizer, electrostatic electron suppression is efficient. Also, magnetic separation and deflection of both species by a 1-kG magnetic field are efficiently applicable. Under suitable energy recovery conditions, perfect collection of both positive and negative ion beams is theoretically achievable, even for a collector voltage of ±480 kV, resulting in 96% energy recovery efficiency. Within ±10% deviation from the reference parameters, the designed BDC shows excellent performance for such parameters as magnetic fields, incident beam energies, and gas line densities. Secondary electrons emitted from the negative ion collector for D− collection are also almost completely prevented from escaping if an auxiliary electrode controlling local electric field near the electrode surface is used.