In this study, a gas-kinetic BGK scheme for the solution of 3-D viscous flows on unstructured hybrid grids is presented. The second order accurate finite volume formulations are given. In order to accurately resolve the boundary layers in wall bounded viscous flows, hexahedral grid cells are employed in the boundary layer regions normal to solid surfaces while the rest of the domain is discretized by tetrahedral cells. The computation time, which is an important deficiency of gas-kinetic BGK schemes, is improved by performing computations in parallel. The parallel algorithm for unstructured hybrid grids is based on the domain decomposition. Several numerical validation cases are presented to show the accuracy and robustness of the proposed approach.