The Bayan Obo deposit in China hosts the world’s largest rare earth element (REE) resource. Age dating results for Bayan Obo range across approximately one billion years (from ∼1.4 to 0.3 Ga), with three age groups (∼1.3 Ga, ∼0.45–0.40 Ga, and 0.28–0.26 Ga). Carbonatite dated to around 1.3 Ga and granitoids to approximately 270 Ma have been identified. The Early Paleozoic vein-type mineralization is widespread in the deposit. However, magmatic activity related to the highest age peak at ∼0.4 Ga has not well been identified in the deposit, complicating the interpretation of the ore genesis. In this study, we report a zircon 232Th-208Pb age of 435.2 ± 4.6 Ma (MSWD = 1.9, N = 26) from carbonatite in Bayan Obo. The zircon morphology, characterized by bipyramidal crystal forms, low U concentrations (mostly < 1 ppm), high Th/U ratio, and carbonatite-like oxygen isotopes (5.92 ± 0.31 ‰), demonstrates that the zircon crystallized from carbonatitic magmas, thus their ages represent the timing of magmatic activity. Although remelting of the Mesoproterozoic carbonatite during Paleozoic carbonatite has been previously documented, the newly identified Early Paleozoic carbonatite derives from a different mantle source, as indicated by their more radiogenic Hf isotope compositions. This suggests that the Bayan Obo deposit experienced multiple carbonatitic activities. The Early Paleozoic carbonatitic activity may have facilitated element mobilization and mineral recrystallization, improving the exploitable levels of the world’s largest REE deposit.