With the goal of lower emissions, hybrid electric propulsion (HEP) aircraft is considered to be a promising solution, with the advantages of being more environmentally friendly and efficient. Moreover, superior reliability and good safety of the HEP systems is vital to ensure a safe flight. For this purpose, this article presents several successful case studies on overspeed, overvoltage/overcurrent, and communication protection with the combination of theory and experimental data. Given the practical application capability of fault protection, this article established a 100 kW HEP platform and designed an effective system level fault protection architecture, which consists of physical layer, decision layer and execution layer. Experimental studies have been conducted on the turboshaft engine overspeed, electrical architecture overvoltage/overcurrent, communication faults to verify the effectiveness of the proposed fault protection scheme. The test results have shown that the proposed strategy can effectively deal with various fault situations mentioned above to prevent the entire HEP aircraft system from becoming paralyzed, thus improving the reliability and safety of the system.