The Mura-Zala Basin is situated on the western margin of the Pannonian Basin and is the most prospective area for hydrocarbon exploration in Slovenia. Multiple source rock studies have been carried out in the area and 1D and 2D numerical models of the thermal evolution of the basin were established in the past. Together with a newly available 3D geometric model of the Mura-Zala Basin, the available data was integrated, refined and combined in a 3D petroleum system model. This allows evaluation of the thermal history in the 3D space. Two hydrocarbon generation scenarios with different source rock distributions and kinetic data sets were conducted. In Karpatian and Early Badenian times, strongly elevated heat flow in the north (between Maribor and Gora Radgona) and the south-east of the basin (Lendava area) probably led to an early hydrocarbon generation phase at these locations. Heat flow decreased until Sarmatian time and stayed at values between 50 and 80 mW/m² until today. A second, major stage of hydrocarbon generation started about 8 Ma ago due to deep burial and generation continued at least until the post-Pontian basin inversion. The youngest formation that became mature is the turbiditic sequence of the Lendava Formation (Pannonian). The structure defining the most important oil and gas field in Slovenia, the Petisovci-Dolina field, only formed during post-Pontian basin inversion. Modeling of hydrocarbon accumulations shows, that the known hydrocarbon deposits cannot be charged from the known Miocene source rocks alone. Therefore, the model favours the idea of an additional pre-Miocene source rock. Alternatively, a far superior source rock may be present in the Miocene succession, which was not drilled so far.