In this study, a parallel implementation of gas-kinetic Bhatnagar-Gross-Krook method on two-dimensional hybrid grids is presented. Boundary layer regions in wall bounded viscous flows are discretised with quadrilateral grid cells stretched in the direction normal to the solid surface while the rest of the flow domain is discretised by triangular cells. The parallel solution algorithm on hybrid grids is based on the domain decomposition using METIS, a graph partitioning software. The flow solutions obtained in parallel significantly improve the computation time, a significant deficiency of gas-kinetic methods. Several validation test cases presented show the accuracy and robustness of the method developed.