The recent miniaturization of components in manufacturing has increased the production of lightweight and sophisticated systems in many different industrial fields. Micro-electro discharge machining (micro-EDM) is a technology widely used for these applications. Although it is a well-known technology, there are still a few research works which investigate the economic implications of this process. This paper reports a model to estimate micro-EDM costs, including both fixed and variable costs. The aim of this model is to estimate the overall manufacturing costs, taking into account production and manufacturing process, tool and workpiece information. A process-based cost calculation method is used for this purpose. The model was applied to two case studies, based on the execution of micro holes, performed on stainless steel and tungsten carbide plates using different electrode materials. The capability of the model was finally demonstrated.