We numerically solve the Navier–Stokes equations to study the rarefied gas flow in short micro- and nanoscale channels. The inlet boundary conditions play a critical role in the structure of flow in short channels. Contrary to the classical inlet boundary conditions, which apply uniform velocity and temperature profiles right at the real channel inlet, we apply the same inlet boundary conditions, but at a fictitious position far upstream of the real channel inlet. A constant wall temperature incorporated with suitable temperature jump is applied at the channel walls. Our solutions for both the classical and extended inlet boundary conditions are compared with the results of other available Navier–Stokes and lattice Boltzmann solvers. It is shown that the current extended inlet boundary conditions can effectively improve the thermofluid flow solutions in short micro- and nanoscale channels.