The thermal structure of continental crust is a critical factor for geothermal exploration, hydrocarbon maturation and crustal strength, and yet our understanding of it is limited by our incomplete knowledge of its geological structure and thermal properties such as hydrogeologic and thermo-mechanical feedbacks that come into play. One of the most critical parameters in modelling upper crustal temperature is thermal conductivity, which itself exhibits strong temperature dependence. In this study, we integrate new laboratory measurements of the thermal conductivity of Sydney Basin rocks under varying temperatures, with finite-element geothermal models of the Sydney Basin using deal.II (Bangerth et al. in ACM Trans Math Softw (TOMS) 33:24, 2007). Basin geometry and structure are adapted from Danis et al. (Aust J Earth Sci 58:517–42, 2011), which quantified the extent of Triassic sediment, Permian coal measures, Carboniferous volcanics and thickness of the crystalline crust. We find that temperature-dependent thermal conductivity results in lower lateral variations in temperature compared to constant thermal conductivity models. However, the average temperatures at depth are significantly higher when temperature-dependent thermal conductivity effects are included. A number of regions within the Sydney Basin demonstrate temperatures above 150 °C at depths of less than 2000 m in these models, for instance NW of Singleton, exhibits a strong thermal anomaly, demonstrating the potential for geothermal prospectivity of the region from experimentally constrained thermal parameters.