This paper analyzes the effect of axial heat conduction on the thermal performance of a balanced counter flow microchannel heat exchanger. The ends of the wall separating the coolants are subjected to the mixed-boundary condition. Analytical equations were developed for predicting the axial temperature of the fluids and the wall as well as the effectiveness of the fluids. Moreover, equations for determining the heat transferred between the heat exchanger and its surroundings have been provided in this paper. The effectiveness of the fluids depended on the NTU, axial heat conduction parameter, manifold fluid temperatures and Biot numbers (of the manifolds). By varying the Biot number the model presented here can be used for designing a MCHXcf with Dirichlet, Neumann or mixed boundary condition at the ends of the wall separating the coolants. At very low values of Biot number the end walls act as if they are insulated. At these values of Biot numbers the effectiveness of the fluids degraded with increase in axial heat conduction parameter for a particular NTU. At very high values of Biot number the end walls assume a temperature that is close to the temperature in the manifold. At high values of Biot number the effectiveness of the fluids can either improve or degrade depending on the manifold temperatures. Moreover, the model developed in this paper has been verified using existing models that consider either adiabatic or isothermal condition at the end walls.