Current models for unconformity-associated uranium deposits predict fluid flow and ore deposition along reactivated faults in >1.76 Ga basement beneath Mesoproterozoic siliciclastic basins. In frontier regions such as the Thelon Basin in the Kivalliq region of Nunavut, little is known about the sub-basin distribution of units and structures, making exploration targeting very tenuous. We constructed a geological map of the basement beneath the unconformity by extrapolating exposed features into the subsurface. The new map is constrained by detailed geological, geophysical, and rock property observations of outcrops adjacent to the basin and by aeromagnetic and gravity data over the geophysically transparent sedimentary basin. From rock property measurements, it is clear that the diverse magnetic and density characteristics of major rock packages provide quantitative three-dimensional constraints. Gravity profiles forward modelled in four cross sections define broad synforms of the Amer Belt and Archean volcanic rocks that are consistent with the structural style outside the basin. Major lithotectonic entities beneath the unconformity include: supracrustal rocks of the Archean Woodburn Lake group and Marjorie Hills meta sedimentary gneiss and associated mixed granitoid and amphibolitic gneiss; the Amer Mylonite Zone and inferred mafic intrusions oriented parallel and sub-parallel; other igneous intrusions of 2.6 Ga, 1.83 Ga, and 1.75 Ga vintage; and the <2.3 Ga to >1.84 Ga Amer Group. Four main brittle regional fault arrays (040°–060°, 075°–90°, 120°, and 150°) controlled development and preservation of the basin. The reactivated intersections of such faults along fertile basement units such as the Rumble assemblage, Marjorie Hills assemblage, Nueltin igneous rocks, and Pitz formation are the best targets for uranium exploration.