Hydrogen fuel cell buses (FCBs) and battery electric buses (BEBs) represent two types of zero-emission drivetrains for air pollution reduction and decarbonization of public transport. In this work, the two bus technologies are compared in terms of their environmental, economic and operational performance. Real-world data from two European sites serve as basis for a carbon footprint (CF) calculation, a total cost of ownership (TCO) analysis and a performance assessment. The results indicate an advantageousness of BEBs compared to FCBs regarding greenhouse gas emissions and costs. The main reason for the higher climate impact of FCBs is the additional energy required to produce hydrogen, compared to the direct use of electricity in BEBs. The BEBs’ advantage in terms of TCO is mainly due to lower vehicle and energy costs. However, the results highly depend on the specific local conditions and assumptions. Furthermore, operation conditions such as range as well as flexibility play a decisive role in bus operators’ decision making. Here, FCBs show considerable advantages, making them favorable for long and/or demanding routes.