This research develops a gas-kinetic Navier-Stokes solver for simulation of hypersonic flows in thermal and chemical non-equilibrium. The Navier-Stokes solvers adopted in current hypersonic CFD codes like LAURA and GASP use a Riemann solver for the convection part and a central difference scheme for the diffusion part. As a result, their integration with DSMC in the transitional and rarefied flow regimes may cause an artificial flow across the interface between CFD/DSMC zones because of the inconsistency in the estimated fluxes. On the other hand, the proposed gas-kinetic BGK solver for the Navier-Stokes equations (BGK-NS) computes the inviscid and viscous fluxes as a single entity, consistent with the DSMC approach. Furthermore, the accuracy of this BGK-NS solver has been demonstrated for hypersonic heat transfer prediction. The approach has also been successfully extended for solution of the Burnett equations whereas the macroscopic Burnett approach has some numerical difficulties. The research further extends this BGK-NS solver to hypersonic flows in thermal and chemical non-equilibrium. In a Phase I SBIR, a prototype non-equilibrium BGK-NS solver has been successfully developed for the nitrogen shock dissociation cases. We propose extension of the solver to three-dimensional cases using the discontinuous Galerkin approach.