One of the major issues associated with the implementation of direct-current distribution systems is the design of a proper protection scheme. The fault current characteristics in direct-current distribution systems are quite different than those in conventional alternating-current grids. Thus, the performance of conventional protection schemes can adversely be affected, and it is necessary to modify the conventional protection schemes or design new protection methods for direct-current networks. This paper proposes a multi-zone differential protection scheme for direct-current distribution systems embedding distributed generators. The proposed method provides a selective and fast protection through the use of a communication link between two sides of a protected feeder. Moreover, the method provides a differential-based backup for the adjacent relays, which can enhance the protection system reliability. In addition, the method proposed in this paper also utilizes directional over-current elements to provide backup protection if the communication network fails. The effectiveness of the proposed protection scheme is evaluated through comprehensive hardware-in-the-loop simulation studies to obtain more realistic results and to investigate the impact of the communication delay. The results show that the proposed method can provide a selective and fast protection and effectively protect components of direct-current distribution systems against different types of faults.