We demonstrate that the parallel computing with graphic processing unit (GPU) effectively accelerates a particle-based carrier transport simulation called EMC/MD method. The simulation speed is increased by parallelizing the point-to-point Coulomb’s force calculation, which is sufficient to accomplish a device characteristic simulation of nanostructured metal-oxide-semiconductor field effect transistor (MOSFET) including source and drain diffusion regions. The EMC/MD simulation powered by GPU computing is a useful tool to investigate the statistical variability analysis of nano-scale transistors.