The time-dependent characteristics of pressure-driven nitrogen flow in long microchannels under uniform wall heat flux input are numerically studied. The two-dimensional momentum and energy equations are solved, with variable properties, rarefaction, involving velocity slip, thermal creep and temperature jump, compressibility, and viscous dissipation effects taken into account. Two cases of unsteady convection are studied. The first one arises due to a sudden heat flux change at the channel wall and the second due to a sudden inlet pressure change. The resulting thermal field and fluid dynamics are determined, described, and discussed in detail. The approach to steady-state conditions and the overall transient response are investigated. It is found that the transient response for the case with a sudden increase in wall heat flux input is slower than that for the case with a sudden decrease in wall heat flux input. The transient response for the case with a sudden increase in inlet pressure is much faster than that for the case with a sudden decrease in inlet pressure. These trends are quantified and discussed on the basis of the underlying transport mechanisms. The difference in overall transient response is caused by the flow rate change and the energy taken up by the pressure work.