Catenary-free tram with supercapacitor for short-distance travel is an emerging and energy-efficient way of urban transportation. However, a large number of decentralized and high-power charging loads from Catenary-free trams bring new challenges to the power system. In addition, frequent and high-voltage charging may result in a shorter lifetime of the supercapacitor. Thus, how to coordinate the charging processes of Catenary-free trams considering the power system constraint and the operation costs of the transportation system is an important open issue, especially as the charging requirements are time-varying. In this paper, we design a charging scheduling system to manage the charging processes of Catenary-free trams. Then, based on the historical and estimated operation data of Catenary-free trams, we propose a day-ahead optimal charging scheduling scheme to arrange their charging processes and report to the power system on the upper bound of the charging loads. Thereafter, we propose a real-time optimal charging scheduling scheme according to the real-time operation information to update the real-time charging loads of Catenary-free trams, such that a trade-off among the electricity cost, operation reliability, and battery lifetime is made to minimize the total operation costs. Finally, simulations have been conducted to evaluate the performance of the proposed charging scheduling schemes and show that the proposed algorithms can reduce the total operation cost by about 28%.