Electric vehicles (EVs) have been widely introduced into the bus fleet while the short driving range and long charging time for battery electric buses (BEBs) are the two main barriers. Thus, bus operators are considering alternatives. Hydrogen buses (HBs) could be a promising option because of their longer driving range and shorter refueling time compared to BEBs. However, introducing HBs would be costly and thus it remains unclear which fuel option (hydrogen or electricity) is more feasible for an electrified public transit system. In response, this study proposed a data-driven micro-simulation approach to compare the system cost and level of service (i.e., the delay time of deviating from the timetable caused by charging events) with different fuel options (electricity or hydrogen) for electrifying public transit, using real-world bus operation information extracted from a GPS bus trajectory dataset in Shenzhen, China. The results suggested that the charging demands of BEBs tended to be concentrated in the central and northwest areas of the city while the refueling demands of HBs were more evenly distributed in not only the center but also the southwest and northeast areas. These resulted in different layouts of charging/hydrogen stations accordingly. Furthermore, given almost the same level of service to maintain, the system cost of the HB scenario could be 48.2% higher than that of the BEB scenario. Therefore, BEBs tended to be more economically feasible in Shenzhen.