The Khanlogh deposit in the Cenozoic Quchan-Sabzevar magmatic belt, NE Iran, is hosted by Oligocene granodioritic rock. The Khanlogh intrusive body is I-type granitoid of the calc-alkaline series. The orebodies are vein, veinlet, massive, and breccia in shape and occur along the fault zones and fractures within the host rock. Ore minerals dominantly comprise magnetite and apatite associated with epidote, clinopyroxene, calcite, quartz, and chlorite. Apatites of the Khanlogh deposit have a high concentration of REE, and show a strong LREE/HREE ratio with a pronounced negative Eu anomaly. Magnetites have a high concentration of REE and show weak to moderate LREE/HREE fractionation. They are comparable to the REE patterns in Kiruna-type iron ores and show an affinity to calc-alkaline magmas. The Khanlogh deposit is similar in the aspects of host rock lithology, alteration, mineralogy, and mineral chemistry to the Kiruna-type deposits. Field observations, hydrothermal alteration halos, style of mineralization, and the geochemical characteristics of apatite, magnetite, and host rock indicate that these magnetite veins have hydrothermal origin similar to Cenozoic Kiruna-type deposits within the Tarom subzone, NW Iran, and are not related to silica-iron oxide immiscibility, as are the major Precambrian magnetite deposits in central Iran.