The purpose of this paper is to show some routes in describing the mechanism responsible for the formation of the temperature difference ΔT at the boundaries of the microfluidic hybrid aligned nematic (HAN) channel, initially equal to zero, if one sets up the stationary hydrodynamic flow vst or under the effect of an externally applied shear stress (SS) to the bounding surfaces. Calculations based on the nonlinear extension of the classical Ericksen–Leslie theory, supplemented by thermomechanical correction of the SS σzx and Rayleigh dissipation function while accounting for the entropy balance equation, show that the ΔT is proportional to the heat flux q across the HAN channel and grows by up to several degrees under the influence of the externally applied SS. The role of vst=ust(z)i^ with a sharp triangular profile ust(z) across the HAN in the production of the highest ΔT is also investigated.