A 3D petroleum systems model of the northern Bonaparte Basin indicates that the potential Nancar Trough source kitchen could be currently expelling hydrocarbons from numerous Jurassic source rocks into traps on the Laminaria High. Based on a range of kinetic models defined for such source rocks within the Plover, Laminaria and Frigate formations, two phases of hydrocarbon generation are predicted. Source rocks within the Lower Cretaceous Echuca Shoals Formation are immature for hydrocarbon generation in this region. Hydrocarbon generation in the Laminaria High commenced during the mid to late Cenozoic, and in the Nancar Trough during the Early Cretaceous, in response to elevated heat flow during the syn-rift phase. The second and main phase of hydrocarbon generation and expulsion started in the mid-Eocene and is ongoing. This phase was controlled by deposition of the thick Cenozoic carbonate shelf, which resulted in deep burial and continued heating of the Mesozoic source rocks. This second phase of expulsion coincided with the reactivation of fault-bounded traps, the consequence of which is that either some or all of the initially trapped hydrocarbons have escaped out of the charged structures. Thus, the most plausible explanation for the occurrence of under-filled and dry structures within the study area is that the faults bounding these traps remained permeable from the late Miocene to the present-day. Secondary alteration processes including water washing and phase fractionation are necessary to explain the bulk composition of Laminaria High and neighbouring under-saturated light oil accumulations.