The activities of the Department of National Defence (DND) account for more than half of the Government of Canada's greenhouse gas emissions. This research examines a clean energy propulsion solution to DND’s carbon footprint using a Proton Exchange Membrane fuel cell (PEMFC) battery hybrid powertrain for military armoured vehicles as a means of meeting Canada's Greening Defence initiatives. Real-world military vehicle operational data is used to create the operation profile for military vehicle powertrain design requirements. Following the model-based design (MBD) approach, the vehicle dynamics, fuel cell system and powertrain system models implemented in MATLAB/Simulink are used to predict the vehicle's performance, emissions, and operational costs. This research examines the feasibility of using a fuel cell-battery electric powertrain for a military armoured vehicle and produces a feasible design solution to meet the identified vehicle operation and performance requirements. The fuel cost and powertrain component performance degradations are modelled to predict the operation costs of the clean vehicle with the benefits of reduced emissions, noise and thermal profiles. The results of this research suggest there are viable, clean propulsion system and energy storage system (ESS) configurations that satisfy the requirements of the operational profile of military armoured vehicles. This research serves as a foundation for the use of clean military vehicle propulsion in Canada.