In the Kutai Basin, regional compression reactivated basement extensional faults, inverting the Paleogene depocenters as anticlines that are often flanked on one side by basement thrusts. Over most of the basin, the overlying Neogene section is detached near the top of an overpressured zone and deformed as a thin-skinned fold-thrust belt. Fieldwork and hydrocarbon exploration on the northern margin of the Kutai Basin, where the sedimentary section is relatively thin compared with the basin center, has provided data in an imaging window where both structural deformation styles can be observed. We contend that even in the deeper parts of the basin center, basement-involved inversion beneath the overpressure zone has influenced the shallower structures that are present in the Mahakam Delta depocenter. In the Mahakam Delta depocenter, the subsequent response to inversion of the Paleogene rift section was controlled in part by heterogeneity in the shallow section, including structures formed through syndepositional loading, delta progradation, normal faults, and marked facies changes. It is proposed that the structural model derived from study of the northern area is applicable to all of the Kutai Basin, including the basin depocenter, an area where only the thin-skinned deformation can be imaged because of the thickness of the Neogene section.