Curie point depth (CPD) mapping in Yukon was done using public domain aeromagnetic data from Natural Resources Canada. CPD mapping estimates the depth in the Earth’s crust to the Curie point temperature (~580°C) where magnetization in rocks disappears. When used in combination with other data, such as heat flow, CPD mapping can serve as a regional scale geothermal prospecting tool. In this study, two different CPD methodologies were employed using two different window sizes (200 km and 300 km). Qualitatively, the results were broadly consistent regardless of the method or window size. South-central Yukon exhibits shallow CPD values while northern and southeastern Yukon have deeper CPD values. This suggests that south-central Yukon has higher levels of heat flow in the mid-to-lower crust compared to the rest of the territory. The CPD results are largely consistent with heat flow measurements from the near surface. Specifically, regions with shallow CPD estimates correspond to areas with elevated heat flow measurements. Geologically, the regions with shallow CPD correspond to the Cordillera, while deep CPD areas appear to be co-located with continental platform rocks of Ancestral North America. Comparison with Yukon-specific crustal geotherms derived from other data suggest that the CPD estimates for south-central Yukon are systematically too deep by 2 to 12 km. The discrepancy is likely caused by the need to better understand and account for the fractal distribution of magnetization in the crust in Yukon. The results of this CPD study are valuable in that 95% of Yukon has been demarcated into regions of shallow CPD (higher heat flow) and deep CPD (lower heat flow). These findings should be combined with other data, such as heat generation and sediment thickness estimates, to identify the most prospective regions of elevated subsurface heat in Yukon.