The energy equation for constant density fluid flow with the viscous dissipation term is often used for the governing equations of gas flow with low velocity in microchannels. If the gas is an ideal gas with low velocity, the average temperatures at the inlet and the outlet of an adiabatic channel are the same based on the first law of the thermodynamics. If the gas is a real gas with low velocity, the average temperature at the outlet is higher or lower than the average temperature at the inlet. However, the outlet temperature which is obtained by solving the energy equation for constant density fluid flow with the viscous dissipation term is higher than the inlet gas temperature, since the viscous dissipation term is always positive. This inconsistency arose from choice of the relationship between the enthalpy and temperature that resulted in neglecting the substantial derivative of pressure term in the energy equation. In this paper, the energy equation which includes the substantial derivative of pressure term is proposed to be used for the governing equation of gas flow with low velocity in microchannels. The proposed energy equation is verified by solving it numerically for flow in a circular microtube. Some physically consistent results are demonstrated.