The Bongor Basin in southern Chad is one of the Cretaceous–Paleogene rift basins developed on the Precambrian crystalline basement and has been confirmed as a petroliferous basin in the last decade. Less than 400 m of Cenozoic unconsolidated sediments are separated by an unconformity from an underlying section of Lower Cretaceous units, in turn separated by another unconformity from underlying Precambrian basement. In addition, there is a locally low-angle unconformity within the Cenozoic section. A synthesis of apatite fission-track analysis data in four wells from the basin reveals two cooling episodes from Late Cretaceous to early Paleocene (beginning between 75 and 60 Ma) and mid-Miocene, respectively. The results suggest that regionally synchronous cooling is a likely scenario. The first exhumation between 75 and 60 Ma affected the whole basin, and the magnitude of uplift and erosion was approximately 1100–1250 m across the whole basin. In contrast, the second exhumation during the Miocene affected mainly the northern part of the basin while the magnitude was weak and could not be detected in the southeast of the basin. Potential trapping structures, for example, fault blocks and synsedimentary anticlines, formed prior to and inverted anticlines as a result of the first cooling phase of exhumation (strong compressional inversion) and were available for hydrocarbon migration and accumulation during the main phase of hydrocarbon generation. The Miocene exhumation was less pronounced and had weak or no impact on the hydrocarbon generation and accumulation.