Electrical discharge micromachining (micro-EDM) is an ideal process for obtaining burr-free machined micron-size apertures. Molybdenum is one of the most attractive high energy and power aperture materials due to its mechanical and physical properties, mainly its high melting temperature and relatively high thermal conductivity. In this paper, fundamental machining characteristics for micro-EDM of molybdenum were investigated both numerically and experimentally. A thermo-numerical model was created to simulate a single spark discharge process. Experimental crater size is investigated using scanning electron microscopy and optical evaluation methods. The effects of important EDM parameters such as the pulse duration on crater shape, temperature distribution, tool wear percentage, and eroded volume were studied. Correlations between numerical and experimental data are also discussed. The model effectively estimates the size of single spark craters in molybdenum. The results show that the developed thermo-numerical model can be an effective tool in predicting the size of a crater formed by a single spark discharge in the micro-EDM process.