The thermal model of a balance counter flow microchannel heat exchanger subjected to external heat transfer and axial heat conduction is modeled in this paper. Three governing equations are developed, one for each of the two fluids and the third for the wall separating the fluids. The ends of the wall separating the fluids are assumed to be insulated. The equations are solved numerically using finite difference method. The model developed in this paper is verified using the conventional effectiveness-NTU equations and existing models that consider each of these effects individually. The combined effect of axial heat conduction and external heating always degraded the hot fluid effectiveness for all values of NTU. Irrespective of NTU the cold fluid effectiveness either increased or decreased depending on whether the degradation in heat gain due to axial heat conduction was compensated by external heat transfer.