This paper presents a micro-electrodischarge machining (EDM) melt-pool model to predict workpiece (anode) material removal from a single discharge micro-EDM process. To model the melt-pool, heat transfer and fluid flow equations are solved in the domain containing dielectric and workpiece material. A level set method is used to identify solid and liquid fractions of the workpiece material when the material is molten by micro-EDM plasma heat flux. The plasma heat flux, plasma pressure and the radius of the plasma bubble have been estimated by a micro-EDM plasma model and serve as inputs to the melt-pool model to predict the volume of material removed from the surface of the workpiece. Experiments are carried out to study the effect of interelectrode voltage and gap distance on the crater size. For interelectrode voltage in the range of 200–300 V and gap distance of 1,2 μm, the model predicts crater diameter in the range of 78–96 μm and maximum crater depth of 8–9 μm for discharge duration of 2 μs. The crater diameter values for most of experimental craters show good agreement with the simulated crater shapes. However, the model over-predicts the crater depths compared to the experiments.