Silica-bearing magnetite was recognized in the Copiapó Nordeste prospect as the first documented occurrence in Chilean iron oxide–copper–gold (IOCG) deposits. The SiO2-rich magnetite termed silician magnetite occurs in early calcic to potassic alteration zones as orderly oscillatory layers in polyhedral magnetite and as isolated discrete grains, displaying perceptible optical differences in color and reflectance compared to normal magnetite. Micro-X-ray fluorescence and electron microprobe analyses reveal that silician magnetite has a significant SiO2 content with small amounts of other “impure” components, such as Al2O3, CaO, MgO, TiO2, and MnO. The oscillatory-zoned magnetite is generally enriched in SiO2 (up to 7.5 wt %) compared to the discrete grains. The formation of silician magnetite is explained by the exchange reactions between 2Fe (III) and Si (IV) + Fe (II), with the subordinate reactions between Fe (III) and Al (III) and between 2Fe (II) and Ca (II) + Mg (II). Silician magnetite with high concentrations of SiO2 (3.8–8.9 wt %) was similarly noted in intrusion-related magmatic–hydrothermal deposits including porphyry- and skarn-type deposits. This characteristic suggests that a hydrothermal system of relatively high-temperature and hypersaline fluids could be a substantial factor in the formation of silician magnetite with high SiO2 contents.