Todays protection schemes for shipboard applications, such as the zone-based differential protection, are efficient, fast, and reliable for fault detection. However, these protection schemes do not consider the system stability or power balance problems that occur with fault isolation and the system reconfiguration. This thesis focuses on developing the extended protection function including the fast reconfiguration function that intends to maintain the power balance of the unfaulted subsystem. Graph theory is utilized to represent the shipboard power system topology in matrices, and matrix operations are developed to represent the corresponding power system topology change and evaluate the outcome of the fault. Intelligent search algorithms are implemented to find the possible system configuration after fault isolation with balanced power generation and load through merging possible connected systems and priority-based load shedding. The algorithms are successfully implemented in MATLAB miles and tested on various shipboard power system configurations and fault scenarios.