The unique, giant, rare earth element (REE) deposit at Bayan Obo, northern China, is the world’s largest REE deposit. It is geologically complex, and its genesis is still debated. Here, we report in situ Th-Pb dating and Nd isotope ratios for monazite and Sr isotope ratios for dolomite and apatite from fresh drill cores. The measured monazite ages (361–913 Ma) and previously reported whole-rock Sm-Nd data show a linear relationship with the initial Nd isotope ratio, suggesting a single-stage evolution from a Sm-Nd source that was formed before 913 Ma. All monazites show consistent εNd(1.3Ga) values (0.3 ± 0.6) close to those of the adjacent 1.3 Ga carbonatite and mafic dikes. The primary dolomite and apatite show lower 87Sr/86Sr ratios (0.7024–0.7030) than the recrystallized dolomite (0.7038–0.7097). The REE ores at Bayan Obo are interpreted to have originally formed as products of ca. 1.3 Ga carbonatitic magmatism and to have undergone subsequent thermal perturbations induced by Sr-rich, but REE-poor, metamorphic fluids derived from nearby sedimentary rocks.