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The Choghart iron oxide–apatite (IOA) deposit is one of the largest iron mines of the Bafq district in Central Iran. This deposit is hosted by the Early Cambrian rhyolites, and diabase dikes crosscut both host rocks and the ore bodies. The Choghart rhyolites erupted in a continental arc setting, while the Choghart diabase dikes formed in a back‐arc basin environment. Thorite, minor titanite, and REE‐oxide are the main hosts of Th and REEs. The mineralogy and geochemistry support that the Th–REE mineralization formed at relatively reduced conditions. The presence of calcite accompanied by thorite and titanite suggests that Th and REE probably migrated as carbonate complexes in the mineralizing hydrothermal fluids. Microthermometric data of calcite associated with thorite indicate that the salinity of the ore‐forming fluids varies from 20 to 30 wt% NaCl equivalent with temperature estimates between 300 and 370°C. The narrow range of homogenization temperature and low salinities of the fluid inclusions imply the presence of only one fluid phase in the Th–REE mineralization. The calcite δ13CPDB (−3.9 to −4.1‰) and δ18OSMOW (6.6–7.0‰) support a magmatic source for the ore‐forming fluids. Actinolite δD (5.55–6.72‰) and δ18O (−100.8 to −82.4‰) also suggest a magmatic source of the ore‐forming fluids. Microthermometric data imply that fluid–rock interaction and cooling were critical factors triggering the thorite precipitation at Choghart IOA deposit. Stable isotopic data indicate that post‐magmatic fluids derived from rhyolitic magmas played a significant role in the Th–REE mineralization.

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The Bafq district, well-known in the world, is the most important iron province in Central Iran. The Early Cambrian volcano-sedimentary sequence in this district, hosts a lot of mineral deposits such as Kiruna-type iron oxide-apatite (IOA), Fe-Mn exhalative and Pb-Zn SEDEX types. Th-U-REE mineralisation in the Bafq IOA deposits occurs in a variety of element associations, (i) REE-P mineralisation as apatite hosting REE-mineral inclusions, (ii) Th-REE mineralisation as Th-REE minerals (e.g. REE-bearing thorite and titanite), (iii) thorium mineralisation as thorium minerals (e.g. thorite and huttonite), (iv) U-REE mineralisation as U-REE minerals (e.g. uraninite and cleveite) and (v) REE-U-Th mineralisation as REE-U-Th minerals (e.g. davidite and allanite). Two main types of apatite are recognised: apatite with inclusions (dominantly monazite, xenotime and allanite) and inclusion poor/free apatite. The presence of calcite paragenesis with Th-REE, Th and U-Th-REE mineralisation indicates transportation of Th and REEs by carbonate complexes in post-magmatic alkaline fluids.