There have been many studies conducted to replace the conventional internal combustion engine (ICE) with a more efficient engine, due to increasing regulations over vehicles’ emissions. Throughout the years, several external combustion engines were considered as alternatives to these traditional ICEs for their intrinsic benefits, among which are Stirling machines. These were formerly utilized in conventional powertrains; however, they were not implemented in hybrid vehicles. The purpose of this study is to investigate the possibility of implementing a Stirling engine in a series hybrid electric vehicle (SHEV) to substitute the ICE. Exergy analysis was conducted on a mathematical model, which was developed based on a real simple Stirling, to pinpoint the room for improvements. Then, based on this analysis, other configurations were retrieved to reduce exergy losses. Consequently, a Stirling-SHEV was modeled, to be integrated as auxiliary power unit (APU). Hereafter, through an exergo-technological detailed selection, the best configuration was found to be the Regenerative Reheat two stages serial Stirling (RRe-n2-S), offering the best efficiency and power combination. Then, this configuration was compared with the Regenerative Stirling (R-S) and the ICE in terms of fuel consumption, in the developed SHEV on the WLTC. This was performed using an Energy Management Strategy (EMS) consisting of a bi-level optimization technique, combining the Non-dominated Sorting Genetic Algorithm (NSGA) with the Dynamic Programming (DP). This arrangement is used to diminish the fuel consumption, while considering the reduction of the APU’s ON/OFF switching times, avoiding technical issues. Results prioritized the RRe-n2-S presenting 12.1% fuel savings compared to the ICE and 14.1% savings compared to the R-S.