The role of the Middle-Upper Miocene source rocks in the Late Neogene petroleum system of the Pannonian Basin is undoubtedly significant, but it is not entirely understood. Only a few general publications exist that describe these sediments and their importance. We have focused on understanding the Neogene tectono-stratigraphic development and petroleum systems of these relatively small syn-rift grabens in southern Hungary. We have developed a workflow for organic geochemical, seismic, and facies interpretation; basin subsidence; and 3D basin modeling to better understand the Miocene-Pliocene-age petroleum system in a study area. This area fully covers two small-scale (less than size each) troughs filled by syn-rift and postrift deposits in large thickness with significantly different structural histories. During our investigation, six source rock beds were identified and built into the model. Thousands of meters of Lower Miocene, (Karpatian age) sediment accumulated in a “pull-apart,” but later structurally inverted Kiskunhalas Trough in the south, where four moderate- to good-quality (2 wt% estimated original total organic carbon [TOC], 200 HI), dominantly gas-prone, immature to wet gas mature source rock beds were identified. In the overlying Middle Miocene (Badenian age) sediments, generally good quality (2 wt% estimated original [TOC], 300–500 HI, type II and II-S), oil-prone, dominantly oil mature source bed was identified. This layer, as the regional Miocene source rock, is mainly responsible for the known hydrocarbon (HC) accumulations. The 3D basin and petroleum system modeling helped us understand the HC migration into the already-discovered fields as well as identify possible future exploration objects.