Extreme waves, called rogue waves or freak waves, usually occur unexpectedly and with very large wave heights. In recent years, extreme waves were reported not only in deep ocean waters but also in shallow waters, which threaten the safety and intactness of the coastal regions. To prevent the coastal infrastructures and communities from the devastating power of extreme surges and waves, many coastal defense structures were built along the coastline, i.e., submerged permeable breakwaters. However, the number of studies on the hydrodynamic characteristics of a submerged permeable breakwater under the impact of extreme waves is relatively few. In addition, wave focusing has been widely used to generate extreme waves in the past few decades. Hence, as a necessary supplement to the previous research work, the hydrodynamic performance of a submerged permeable breakwater under the impacts of focused wave groups was numerically studied by using a nonhydrostatic numerical wave model (NHWAVE). The influences of several main factors, such as the incident significant wave height, water depth, wave peak period, porosity of the breakwater (n), and the side slope angle of the breakwater, were considered. It is expected that the results of this study will further strengthen the research on the hydrodynamic characteristics of a submerged permeable breakwater under extreme wave conditions.