We investigate the accuracy of two expressions for configurational temperature when calculating thermal transport properties in non-equilibrium systems under thermal gradients. The temperature

, introduced by Jepps et al. [Phys. Rev. E. 62;2000:4757] is found to give results in almost exact agreement with the equipartition temperature for the thermal conductivity of the Lennard-Jones fluid, and for the temperature profile across a solid–liquid interface. Measurements of are, however, less precise than those of the equipartition temperature, which results in less accurate measurements of the interfacial thermal conductance across a liquid–vapour interface. The approximate expression , which depends strongly on the number of sampled atoms, predicts unphysical negative thermal conductances in liquid–vapour interfaces, highlighting the limitations of some definitions of the configurational temperature in the computation of thermal transport properties via non-equilibrium simulations.