In this paper we explore issues in designing a heat exchanger for a microfluidic channel. Among important issues specific to heat exchangers in microfluidics are axial conduction and shear rate dependant phenomena. A heat exchanger has been designed for use in a further study to examine the effect of liquid contact angle on the convective heat transfer coefficient. We show that by applying a constant heat flux to the outer channel wall surface, axial conduction causes the boundary conditions to change from uniform temperature at lower Reynolds numbers, to approach uniform heat flux at higher Reynolds numbers.