Micro-EDM is a thermal energy-based non-contact machining process, able to machine any electrically conductive material, making it one of the preferred methodologies for micro-manufacturing. Before making any improvement in the process, understanding of the process physics is very important. A conservative numerical scheme to model the micro-EDM process using the finite volume method with Fourier heat conduction equation in cylindrical coordinates as the governing equation has been attempted. The model was formulated with Gaussian distribution of input heat flux, temperature-dependent material properties, latent heat and fixed percentage of heat to the workpiece. The proposed numerical scheme was validated with simplified analytical results. Numerical models considering temperature-dependent and temperature-independent thermal conductivity and specific heat were considered. The simulation results showed a near-hemispherical crater. The model was validated experimentally by comparing the numerically simulated craters with experimentally generated ones. Results showed that the numerical model with temperature-dependent material properties was able to predict the crater with the highest accuracy on comparing with the experimental results. The temperature-dependent model predicted the crater dimensions with relative error ranging between 6 and 13% for radius and 3 and 14% for depth.