Fuel cells are very promising technologies for efficient electrical energy generation. The development of enhanced system components and new engineering solutions is fundamental for the large-scale deployment of these devices. Besides automotive and stationary applications, fuel cells can be widely used as auxiliary power units (APUs). The concept of a direct methanol fuel cell (DMFC) is based on the direct feed of a methanol solution to the fuel cell anode, thus simplifying safety, delivery, and fuel distribution issues typical of conventional hydrogen-fed polymer electrolyte fuel cells (PEMFCs). In order to evaluate the feasibility of concrete application of DMFC devices, a cost analysis study was carried out in the present work. A 200 W-prototype developed in the framework of a European Project (DURAMET) was selected as the model system. The DMFC stack had a modular structure allowing for a detailed evaluation of cost characteristics related to the specific components. A scale-down approach, focusing on the model device and projected to a mass production, was used. The data used in this analysis were obtained both from research laboratories and industry suppliers specialising in the manufacturing/production of specific stack components. This study demonstrates that mass production can give a concrete perspective for the large-scale diffusion of DMFCs as APUs. The results show that the cost derived for the DMFC stack is relatively close to that of competing technologies and that the introduction of innovative approaches can result in further cost savings.