U–Pb ages of zircons recovered from Pliocene pyroclastic deposits in northern part of the Cenozoic intra-Carpathian back-arc basin (Pannonian Basin) span the interval from Pliocene (2.2 Ma) to Paleoproterozoic (Orosirian–Rhyacian, 1850–2115 Ma). The scattered U–Pb ages reflect eruption ages of the host basaltic volcanic centres, two episodes of post-Eocene magmatic crustal growth, and the possible tectonic affiliation, provenance and age of the subjacent basement or the sedimentary basin detritus sampled by the basaltic magma. The youngest zircons define the maximum ages of phreatomagmatic eruptions during the Late Miocene–Pliocene extension. These zircons are distinguished from older zircons by Zr/Hf (40–90) and Th/U ratios (0.5–4.5) as well as super-chondritic εHf(t) values ranging from + 7 to + 14, indicating mantle-derived parental magmas. The locally increased Th/U ratios (up to 8) accompanied by Zr/Hf > 60 are diagnostic of evolved phonolite parental melt. Hence, the youngest zircons can be interpreted as antecrysts, originating from evolved melts cogenetic with the host alkali basalts. In contrast, older zircons represent xenocrysts scavenged by the uprising basalt from surrounding rocks. Subordinate Eocene–Early Oligocene (29–38 Ma) sub-group of zircon xenocrysts is coincidental with the magmatism and volcanism along the Periadriatic lineament and the middle-Hungarian zone. The Early Miocene (18 Ma) cluster is coeval with the deposition of the Bükk Mountains felsic ignimbrite correlated with the onset of the back-arc extension that triggered Miocene sedimentation within the Pannonian Basin. The Eocene–Early Oligocene zircons have been likely scavenged from pyroclastic and ash-fall deposits of the Palaeogene retroarc basin subjacent to the Miocene basin infilling. Sub-chondritic εHf(t) values between − 2.5 and − 8 in the Eocene–Early Miocene zircons attest their crystallization from subduction-related felsic-to-intermediate melts containing large amounts of recycled crustal material. Palaeozoic–Proterozoic zircons create a heterogeneous population with variable trace element abundances and εHf(t) values. The determined age clusters are reminiscent of some basement units cropping out recently in Central Western Carpathians. Zircon Hf isotope data indicate recycling of up to 3.4 Ga old mafic crust and also the presence of 2 Ga old juvenile mafic crust. These units had either underlain the northern part of the Pannonian Basin during Pliocene or had been exposed during the deposition of Miocene clastic sediments. The absence of Mesoproterozoic, Grenvillian zircons (0.9–1.8 Ga) in the pre-Cenozoic population of zircon xenocrysts is provisionally interpreted as indicating the evolution of the zircon source area within the west-African Craton.