Abstract The Bayan Obo deposit hosted by the H8 unit is a world-class rare earth element (REE) deposit with considerable niobium (Nb) and iron (Fe). Permian granites are widely exposed in the mining area and have a close spatial association with the Nb mineralization. Whether the granites contributed Nb or only remobilized existing mineralization is important for understanding the controls of ore formation. Previous studies have mostly focused on the REEs, whereas research on Nb has been limited. This is due mainly to the difficulty of accurately determining the age of the Nb mineralization because of the fine-grained and texturally complex nature of the Nb-bearing minerals and their exceptionally low U content. Although microbeam techniques show promise in tackling the aforementioned challenges, their application is hampered by matrix effects caused by the diverse composition of Nb-bearing minerals. Here we report the application of a high-precision secondary ion mass spectrometry (SIMS) Pb-Pb isochron approach that enables young samples (i.e., <500 Ma) to be dated without matrix-matched reference materials. A variety of Nb-bearing minerals from eastern Bayan Obo were analyzed, yielding Pb-Pb isochron ages of 276 ± 10 Ma (pyrochlore, 394–6,864 ppm U in the rim and 6,563–19,858 ppm in the core), 277 ± 36 Ma (fersmite, 18–61 ppm U; fergusonite-Ce, 45–95 ppm U), and 257 ± 46 Ma (aeschynite, 342–1,006 ppm U). In combination with the deposit geology and petrographic observations, these ages link the Nb mineralization to ~270 Ma granites. As these granites are not particularly rich in Nb, skarn formation during granite emplacement is interpreted to have remobilized the existing Nb mineralization, which increased the grain size of the Nb-bearing minerals—a key factor facilitating their extraction. Our study shows that high-precision SIMS Pb-Pb analysis holds promise for directly dating mineralization without matrix-matched reference materials. It also emphasizes the need to consider the role of the Nb remobilization at Bayan Obo and elsewhere.