Hydrogen fuel cells have been previously investigated as a viable replacement to traditional gas turbine auxiliary power unit onboard fixed wing commercial jets. However, so far no study has attempted to extend their applicability to rotary wing aircrafts. To aid in the advancement of such innovative technologies, a holistic technical approach is required to ensure risk reduction and cost effectiveness throughout the product lifecycle. This paper will evaluate the feasibility of replacing a gas turbine auxiliary power unit on a helicopter with a direct hydrogen, air breathing, proton exchange membrane fuel cell, all while emphasizing a system engineering approach that utilize a specialized set of tools and artifacts.