This thesis focuses on the model-based methodology for designing a protection scheme for shipboard power system(SPS) based on instantaneous overcurrent digital relays. To achieve this, an instantaneous overcurrent relay model is first developed in MATLAB/Simulink. Then, the Simulink model is downloaded to the DSP-based platform dSPACE, which runs the Simulink model in real-time, to perform hardware-in-the-loop testing (HIL). Thus, through the dSPACE hardware, the proposed relay model is tested for various fault conditions in three HIL platforms. Different electromagnetic transient real-time digital simulators are used to simulate the SPS, to which protection is provided through the relay modeled in dSPACE. Testing results show that the developed model can work with different real-time platforms, and that in contrast to a commercial relay, the developed relay model has increased flexibility because settings such as reclose delay and pickup value can be changed online.