We use a direct simulation Monte Carlo (DSMC) method to simulate gas heating/cooling and choked subsonic flows in micro/nanoscale channels subject to either constant wall temperature or constant/variable heat flux boundary conditions. We show the effects of applying various boundary conditions on the mass flow rate and the flow parameters. We also show that it is necessary to add a buffer zone at the end of the channel if we wish to simulate more realistic conditions at the channel outlet. We also discuss why applying equilibrium-based Maxwellian distribution on molecules coming from the channel outlet, where the flow is nonequilibrium, will not disturb the DSMC solution. The current velocity, pressure, and mass flow rate results are compared with different analytical solutions of the Navier–Stokes equations. Although there are good agreements between the DSMC results and the analytical solutions in low compressible flow, the analytical solutions yield incorrect velocity and mass flow rate values in short micro/nanochannel flows with high compressibility and/or choked flow conditions.