In recent years, shipboard microgrids (MGs) have become more flexible, efficient, and reliable. The next generations of future shipboards are required to be equipped with more focuses on energy storage systems to provide all-electric shipboards. Therefore, the shipboards must be very reliable to ensure the operation of all parts of the system. A reliable shipboard MG should be protected from system faults through protection selectivity to minimize the impact of faults and facilitate detection and location of faulty zones with the highest accuracy and speed. It is necessary to have an across-the-board overview of the protection systems in DC shipboards. This paper provides a comprehensive review of the issues and challenges faced in the protection of shipboard MGs. Furthermore, given the different types of components utilized in shipboard MGs, the fault behavior analysis of these components is provided to highlight the requirements for their protection. The protection system of DC shipboards is divided into three sub-systems, namely, fault detection, location, and isolation. Therefore, a comprehensive comparison of different existing fault detection, location, and isolation schemes, from traditional to modern techniques, on shipboard MGs is presented to highlight the advantages and disadvantages of each scheme.