Shared autonomous vehicles (SAVs) encompassing autonomous driving technology and car-sharing service are expected to become an essential part of transportation system in the near future. Although many studies related to SAV system design and optimization have been conducted, most of them are focused on shared autonomous battery electric vehicle (SABEV) systems, which employ battery electric vehicles (BEVs) as SAVs. As fuel cell electric vehicles (FCEVs) emerge as alternative fuel vehicles along with BEVs, the need for research on shared autonomous fuel cell electric vehicle (SAFCEV) systems employing FCEVs as SAVs is increasing. Therefore, this study newly presents a design framework of SAFCEV system by developing an SAFCEV design model based on a proton-exchange membrane fuel cell (PEMFC) model. The test bed for SAV system design is Seoul, and optimization is conducted for SABEV and SAFCEV systems to minimize the total cost while satisfying the customer wait time constraint, and the optimization results of both systems are compared. From the results, it is verified that the SAFCEV system is feasible and the total cost of the SAFCEV system is even lower compared to the SABEV system. In addition, several observations on various operating environments of SABEV and SAFCEV systems are obtained from parametric studies.