Mts. Kalnik and Požeška gora volcaniclastic sequences hold valuable information concerning the Miocene syn-rift evolution of the North Croatian Basin, and the evolution of the Carpathian–Pannonian Region and the Central Paratethys. We present volcanological, high-precision geochronological, and compositional data of volcanic glass to constrain their tephrochronology, magmatic provenance, and timing of the initial Central Paratethys flooding of the North Croatian Basin. Based on CA-ID-TIMS U–Pb zircon ages (18.060 ± 0.023 Ma for Mt. Kalnik and 15.345 ± 0.020 Ma for Mt. Požeška gora) and coeval 40Ar/39Ar sanidine ages (18.14 ± 0.38 Ma and 18.25 ± 0.38 Ma for Mt. Kalnik and 15.34 ± 0.32 Ma and 15.43 ± 0.32 Ma for Mt. Požeška gora), Mt. Kalnik rhyolitic massive ignimbrites and Mt. Požeška gora rhyolitic primary volcaniclastic turbidites are coeval with Carpathian–Pannonian Region Miocene post-collisional silicic volcanism, which was caused by lithospheric thinning of the Pannonian Basin. Their affiliation to Carpathian–Pannonian Region magmatic activity is supported by their subduction-related geochemical signatures. Although Mts. Kalnik and Požeška gora volcaniclastics are coeval with the Bükkalja Volcanic Field Csv-2 rhyolitic ignimbrites, North Alpine Foreland Basin, Styrian Basin, Vienna Basin, and Dinaride Lake System bentonites and volcaniclastic deposits, reliable tephrochronological interpretations based on comparison of volcanic glass geochemical composition are not possible due to a lack of data and/or methodological discrepancies. Our new high-precision geochronology data prove that the initial Middle Miocene (Badenian) marine flooding of parts of the North Croatian Basin occurred at least ~ 0.35 Ma (during the NN4 Zone) before the generally accepted ~ 15 Ma maximum flooding age at the basin scale, calibrating the timing of the onset of the widespread “mid-Langhian” Central Paratethys flooding.