Fuel Cell Electric Vehicles (FCEVs) are emerging as capable mobile transportation systems for various heavy duty and high-energy applications such as cars and trucks. FCEVs are needed in the future to slow down climate change and reduce the demand for fossil fuel reserves. Significant adoption of this alternative technology requires denser spatial packaging and efficient thermal management of fuel cells within the automotive system. This paper presents an implementation of a novel 2D physics-based optimal packing and routing (PR) method applied to an industry-relevant application: underhood spatial packaging of an automotive fuel cell system (AFCS) for efficient thermal management. The fuel cell system and related thermal management components present a complex challenge for minimizing package volume while delivering the required vehicle capability and performance. Of particular interest in this work is optimal packing and routing (PR) for thermal management with the goals of minimizing the interconnect hose lengths, the underhood bounding box area, and the number of connections. Several case studies have been demonstrated to minimize the vehicle underhood area occupied by the fuel cell system subject to geometric (component orientation) and physics-based constraints (device temperature, hydraulic pressure loss, etc.). The results show significant improvement in spatial packaging density of the 2D AFCS. Improvements in AFCS spatial packaging density will enable faster and greater adoption of this technology into mobile transportation systems.