The Choghart magnetite-apatite deposit situated in the Bafq district, Central Iran, has been scrutinized for rare earth elements (REEs) by precise geochemical investigation. The Central Iran is a susceptible area of rare earth elements. One of the Choghart’s prominent points is the existence of hydrothermal zones which made prediction of REEs occurrence within the deposit possible. Choghart is placed within felsic volcanic tuffs, rhyolitic rocks, and volcanic sedimentary sections belonging to the lower Cambrian. Abundance and distribution pattern of REEs in Choghart iron deposits reveal a part of deposit formation and its mineralogical modifications. Petrography and mineralogy of the ore body demonstrated two main types of alterations (sodic and calcic) associated with iron ore mineralization in Choghart deposit. The main ore includes a large quantity of massive magnetite in the lower part of Choghart deposit. The minor mineralization involves apatite, pyrite, alkaline amphibole, especially actinolite and tremolite, calcite, talc, quart, monazite, and bastnasite. Geochemical sampling from north–northeast (N-NE) side of the mine denotes the presence of these elements in hydrothermal zones. Statistical populations of the area were categorized by fractal geometry into four main differentiations: host rock type (albitofyre), iron, metasomatose, phosphate zones, and a subset of the phosphate zone which is named high iron high phosphate type. REEs like lanthanum, neodymium, yttrium, and niobium constitute the most quantity of Choghart. Deposit characteristics demonstrate its similarity to Kiruna type. The significant feature of iron oxide-apatite deposits of Kiruna ore type is the existence of monazite inclusions within apatite. These inclusions were also observed within apatite type I and II of Choghart mineralization. Moreover, REEs geochemistry in Choghart deposit was identified by investigation on geochemical data analyses. The analysis represents negative Eu anomaly and further enrichment of light REEs compared to the heavy ones. Chondrite normalized REEs patterns are defined by negative anomalies of Eu, which is the main characteristic of Kiruna ore type. The results showed that REEs concentration in phosphate zone, as a high absorption of REEs, is much higher than metsomatose, albitofyre, and iron zones. REEs distribution in N-NE side of the mine indicated that the contact of iron ore with tailings in N-NW side of the mine leads REEs to be enriched nearly 1% , as well as that of NE with high contents of REEs 1.5% ), which is very significant.