In electric and hybrid-electric aircraft, the battery systems are usually composed of up to thousands of battery cells connected in series or parallel to provide the voltage and power/energy requirements. The inconsistent cells could affect the battery pack and its performance or even endanger electric and hybrid-electric aircraft security; thus, the early fault diagnosis of the battery system is essential. A well-designed battery management system along with a set of reliable voltage and current sensors is required to properly measure and control the cells operational variables in a large battery pack. In this study, based on the battery working mechanism, a new, fast, and robust fault diagnostic scheme is proposed for a lithium-ion battery (LIB) pack that can be employed for applications such as electric and hybrid-electric aircraft. In this method, some faults such as the overcharge, overdischarge occurring in LIB packs can be detected and isolated, based on some predefined factors gained from the battery models in healthy, overcharge, and overdischarge conditions. Finally, the effectiveness of the proposed fast fault diagnosis scheme is experimentally validated with LIBs under a typical flight cycle.