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 over-charge, over-discharge occurring in LIB packs can be detected and isolated, based on some predefined factors gained from the battery models in healthy, over-charge and over-discharge conditions. Finally, the effectiveness of the proposed fast fault diagnosis scheme is experimentally validated with LIBs under a typical flight cycle.