A counterflow heat exchanger model, based on a bayonet-type configuration, has been developed for predicting the performance of small-scale thermal systems. The purpose of the model is to predict how well a counterflow heat exchanger works for isolating high temperatures for devices that might act as miniature combustors, fuel reformers, or micro-reactors. Three thermal loss mechanisms are considered: (1) flow loss due to nonunity effectiveness, (2) thermal conduction along the axial direction, and (3) radiation surface loss to the surroundings. A set of three coupled differential equations were developed for modeling the heat exchanger: one for each of two fluid streams and one for the wall temperature, all as a function of axial position. The wall equation contains a highly nonlinear term linked to radiation surface loss. This study differs from past investigations in several ways. First, the boundary conditions model is a heat exchanger attached to a substrate at ambient temperature and with a hot end free to assume a temperature halfway between the two fluid temperatures. Next, surface radiation is explicitly included to capture heat loss at elevated temperatures. Finally, an implicit method is described that is capable of solving the set of coupled, nonlinear equations. The results of the study are presented in the form of a normalized heat loss term having contributions from the three loss mechanisms. Both conduction and surface radiation losses are shown to be significant in small-scale, high-temperature heat exchangers. For microthermal systems based on the bayonet-type of temperature isolation, this study demonstrates the need for low thermal conductivity materials as well as low effective surface emissivities.