The Bayan Obo REE-Fe-Nb deposit is the world’s largest known REE resource, yet its multi-stage geological evolution remains debated, particularly regarding a distinct Early Paleozoic event. Here, we present high-resolution zircon U-Pb ages and trace-element data obtained through depth profiling analysis on zircons extracted from the carbonatite body at Bayan Obo. Our data reveal a consistent zircon crystallization age of 436.1 ± 6.2 Ma, characterized by homogeneous internal structures without detectable inherited cores or zoning. Geochemical signatures, including extremely low Ti contents (<3 ppm), pronounced positive Ce anomalies (Ce/Ce* typically >10), and substantial enrichment in Y and heavy rare earth elements (HREE), collectively suggest a hydrothermal rather than magmatic origin for this zircon population. Mineralogical mapping reveals a matrix dominated by magnetite and ankerite, with minor apatite and monazite, and no detectable dolomite, pyrochlore, or fluorine-bearing REE-carbonates. This assemblage reflects pervasive fluid-mediated metasomatism under phosphate-rich, and fluorine-poor conditions. Integrating these findings with regional tectonic settings and previous geochronological studies, we propose that the ~430 Ma zircons crystallized from hydrothermal fluids mobilized during tectono-thermal reactivation linked to the Paleo-Asian Ocean closure. This study provides further evidence and understanding of the hydrothermal activity of the Bayan Obo deposit in the Early Paleozoic.