Carboniferous–Permian magmatic rocks are common in the Carpathian–Pannonian region, whereas Cambrian–Devonian (meta)igneous associations are less frequent and not yet confirmed by radiometric data in the basement of the Pannonian Basin. The major goal of this study was to constrain Ordovician zircon U–Pb ages from (meta)igneous rocks representing three prospective study areas in the inner Carpathian–Pannonian region: the Bihor Mts (Apuseni Mts, Tisza–Dacia Mega-unit), the eastern Mecsek Mts (southern Transdanubia, Tisza–Dacia Mega-unit), and the Balaton Highland (central Transdanubia, ALCAPA Mega-unit). Metagranitoids from the Bihor Mts yielded an Early Ordovician protolith age of 478.0 +3.2/−2.5 Ma which, supported by bulk-rock geochemistry and deformation, suggests they belong to the ~495–477 Ma extensional bimodal magmatism of the Biharia terrane and may be related to back-arc rifting along the northeastern margin of Gondwana. These rocks were later overprinted by multiple Alpine shearing events within the Highiş–Biharia Shear Zone. A Middle Ordovician age of 464.8 +3.0/−3.1 Ma, from one of the lower magmatic sections of the Kékkút–4 borehole in the Balaton Highland, is most plausibly attributed to the Alsóörs Metarhyolite and identifies it as the oldest known igneous formation within Hungary confirmed by numerical age data. Contrary to being overlain by Silurian slate, monzonites from the Szalatnak–3 borehole in the eastern Mecsek Mts yielded a Carboniferous age of 332.7 +2.1/−1.6 Ma. These subvolcanic rocks exhibit alkaline, apparently shoshonitic characteristics and are slightly younger than the nearby I-type Mórágy Metagranite (~354–338 Ma). Supported by bulk-rock geochemical similarities, this may indicate that the two formations originated along the same active continental margin, representing different phases of a complex Variscan geodynamic evolution: subduction followed by post-collisional extension.