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The realization of single-molecule thermal conductance measurements has driven the need for theoretical tools to describe conduction processes that occur over atomistic length scales. In macroscale systems, the principle that is typically used to understand thermal conductivity is Fourier’s law. At molecular length scales, however, deviations from Fourier’s law are common in part because microscale thermal transport properties typically depend on the complex interplay between multiple heat conduction mechanisms. Here, the thermal transport properties that arise from electron transfer across a thermal gradient in a molecular conduction junction are examined theoretically. We illustrate how transport in a model junction is affected by varying the electronic structure and length of the molecular bridge in the junction as well as the strength of the coupling between the bridge and its surrounding environment. Three findings are of note: First, the transport properties can vary significantly depending on the characteristics of the molecular bridge and its environment; second, the system’s thermal conductance commonly deviates from Fourier’s law; and third, in properly engineered systems, the magnitude of electron hopping thermal conductance is similar to what has been measured in single-molecule devices.