The Mushgai-Khudag complex is part of the Late Mesozoic Central Asian carbonatite province. Fluorite mineralization is manifested throughout the province, including the Mushgai-Khudag complex. We have investigated the geochemical features and fluid inclusions of fluorites from different types of fluorite-bearing rocks. Fluorite from quartz-fluorite rocks has rare earth element (REE) concentrations in the range of 10500−144300 ppm and the highest light REE contents, with (La/Yb)N = 56−960. Fluorite from the fluorite-apatite-celestine rocks has slightly lower REE enrichment, especially light REE content, with concentrations of 200−5900 ppm and (La/Yb)N = 18−204. Fluorite from the fluorite-calcite rocks is characterized by REE contents of 22−1100 ppm and a variable (La/Yb)N of 0.6−59. These variations in the fluorite REE composition from different types of rocks were probably caused by the fact that at elevated temperatures, fluorine-containing light REE complexes are more stable than fluorine-containing heavy REE complexes. The progressive enrichment of medium and heavy REEs in the latter fluorite is related to fluid evolution. The homogenization temperature and salinity values of ﬂuid inclusions in the Mushgai-Khudag fluorites vary between 550 and 185 °C and from rather high to 2 wt.%, respectively. The parental fluids of the fluorite-bearing rocks evolved from quartz-fluorite rocks to fluorite-apatite-celestine rocks to fluorite-calcite rocks. The key component was changed from sulfate to carbonate-chloride along with the high to medium temperature decrease (∼500−245 °C).