This study uses basin modelling to analyze the hydrocarbon potential of two Neogene sedimentary sub-basins in southern Hungary. The modelling simulated the subsidence and thermal maturation histories. It determined that the southern sub-basin reached greater depths and temperatures, resulting in gas generation from source rocks beginning 11.6 million years ago. Oil generation in the northern sub-basin began more recently around 6.8 million years ago. While hydrocarbons migrated upward along faults, accumulations have only formed so far in the southern sub-basin within anticline structures in carbonate formations. The complex geological evolution and thermal anomalies revealed by the modelling provide new perspectives for hydrocarbon exploration in the area.