Fracture surface topography exhibits long-range spatial correlations resulting in a heterogeneous aperture field. This leads to the formation, within fracture planes, of preferential flow channels controlling flow and transport processes. By means of a 3-D heat transport model coupled with a 2-D fracture flow model based on the lubrification approximation (i.e., local cubic law), we investigate how the statistical parameters determining spatial aperture variations in individual fractures control the heat exchange at the fluid/rock interface and heat transport by flow. Ensemble statistics over fracture realizations provide insights into the main hydraulic and geometrical parameters controlling the hydraulic and thermal behaviour of rough fractures. Similarly to the rough fracture’s hydraulic behaviour, we find that its heat transport behaviour deviates from the conventional parallel plate fracture model with increasing fracture closure and/or decreasing correlation length. We demonstrate that the advancement of the thermal front is typically slower in rough fractures compared to smooth fractures having the same mechanical aperture. In contrast with previous studies that neglect temporal and spatial temperature variations in the rock matrix, we find that the thermal behavior of a rough-walled fracture can, under field-relevant conditions, be predicted from a parallel plate model with an aperture equal to the rough fracture’s effective hydraulic aperture. This greatly simplifies the prediction of possible reservoir thermal behavior when using field measurable quantities and hydrological modeling.