A comprehensive study, including geological mapping, structural and thermochronological analysis, has been carried out on Ivanščica Mountain (NW Croatia), with the aim to reconstruct the tectonic history of the Dinarides, Southern/Eastern Alps and Pannonian Basin transitional zone. Implementation of structural and thermochronological methods enabled a subdivision of Ivanščica Mt. into two structural domains (from bottom to top): Ivanščica Parautochthon and Ivanščica Imbricate Fan and Cenozoic sedimentary cover. In addition, a sequence of deformational events in tectonic history of this transitional zone is proposed, comprising three extensional and four contractional events starting from Middle Triassic until present times. The two oldest deformational events indicate Middle Triassic (D1) and Early Jurassic (D2) extensional pulses and only occur in volcano-sedimentary successions of the Ivanščica Mt. The oldest contractional event (D3) is related to the obduction of a Neotethyan ophiolitic mélange over an Upper Triassic to Lower Cretaceous succession of the eastern margin of the Adriatic microplate, which resulted in thermal overprint of the Ivanščica Imbricate Fan structural domain in Berriasian—Valanginian times (~ 140 Ma). This event was soon followed by a second contractional event (D4), which resulted in thrusting and imbrication of the Adriatic passive margin successions together with previously emplaced ophiolitic mélange, thermal overprint of the footwall successions, fast exhumation and erosion. Apatite fission track data together with syn-tectonic deposits indicate an Hauterivian to Albian age of this D4 event (~ 133–100 Ma). These Mesozoic structures were dextrally rotated in post-Oligocene times and brought from the initially typically Dinaridic SE striking and SW verging structures to the recent SW striking and NW verging structures. The following extensional event (D5) is associated with the formation of SE striking and mostly NE dipping normal listric faults, and ENE striking dextral faults accommodating top-NE extension in the Pannonian Basin. Deformations were coupled with hanging wall sedimentation of Ottnangian to middle Badenian (middle Burdigalian to upper Langhian; ~ 18–14 Ma) syn-rift deposit as observed from the reflection seismic and well data. A short-lasting contraction (D6) was registered in the late Sarmatian (late Serravallian; ~ 12 Ma). The youngest documented deformational event (D7) resulted in reactivation of ENE striking dextral faults, formation of SE striking dextral faults as well as the formation of E to ENE trending folds and reverse faults. This event corresponds to late Pannonian (late Messinian; ~ 6 Ma) to Present NNW-SSE contraction driven by the indentation and counterclockwise rotation of Adriatic microplate. Recognized tectonic events and their timings indicate that Ivanščica was mainly affected by deformational phases related to the Mesozoic evolution of the Neotethys Ocean as well as Cenozoic opening and inversion of the Pannonian Basin. Therefore, the Mesozoic tectono-sedimentary evolution of Ivanščica Mountain proves the paleogeographic affiliation of its non-ophiolitic Mesozoic structural-stratigraphic entities to the Pre-Karst unit of the Dinarides.