The implicit gas-kinetic Bhatnagar–Gross–Krook (BGK) scheme and kinetic boundary conditions are introduced and applied to the study of two typical flows in the near continuum regime, the hypersonic flow around a hollow cylinder flare and the flow in microchannels. The grid convergent numerical results in hypersonic flow agree well with experimental measurements and direct simulation Monte Carlo (DSMC) studies. For the low-speed microchannel flow, the present simulated results show good agreement with analytic solutions deduced from Navier–Stokes (NS) equations with slip conditions and DSMC computations. The implicit technology is found to be able to greatly improve the efficiency, which is expected to be a truly practical tool for the flow in micro-electro-mechanical systems (MEMS). The present study reveals the good performance of the BGK scheme in simulations of both high-speed and low-speed viscous flow in near continuum regime.