The gas-kinetic BGK scheme on unstructured hybrid grids is presented. In order to accurately resolve the boundary layers in wall bounded viscous flow solutions, quadrilateral grid cells are employed in the boundary layer regions normal to solid surfaces while the rest of the domain is discretized by triangular cells. The computation time, which is a significant deficiency of the gas-kinetic schemes, is improved by performing computations in parallel. The parallel algorithm for hybrid grids is based on the domain decomposition using METIS, a graph partitioning software. Several numerical test cases are presented to show the accuracy and robustness of the proposed approach.