New data on the U–Pb age (SHRIMP-II) and trace element composition (SIMS) of zircon from gneisses of the Khapchan Group of the Khapchan terrane of the Anabar Shield are presented. Zircon grains contain relicts of magmatic zircon, the protolith and source areas of which are difficult to specify. The only zircon in this group with the least altered core preserved the 207Pb/206Pb protolith age of 1971 ± 19 Ma. During granulite metamorphism, the zircon was subjected to the impact of fluid enriched in incompatible elements. The disurbances affected both the U–Pb isotope system (zircon age was “reset” at metamorphic age of 1920–1930 Ma) and composition of zircon, magmatic cores of which were significantly recrystallized in a solid state or dissolved by fluid up to the practically complete disappearance of primary zircon. In both the cases, zircon was sharply enriched in incompatible elements (Ca, Ti, Pb, Sr, Ba, and some others) owing to fluid effect, while preserved cores seemed to be rimmed by a new zircon population (CL-black). The REE distribution patterns in the recrystallized cores acquired a “bird’s wing” profile atypical for zircon. When the fluid lost its reactivity, the main part of the zircon grain crystallized, typical of granulite zircon. This zircon population is less enriched in incompatible element than the cores are. The horizontal pattern of HREE distribution is consistently repeated, which indicates the co-crystallization of zircon and garnet. The estimated crystallization temperature of the main part of zircon varies in a narrow range of 800–830°C. All zircon domains in the Wetherill concordia diagram form a single trend with a zero lower intercept and an upper intercept confirmed by concordant cluster with an age around 1920–1930 Ma. This value corresponds to the age of regional Paleoproterozoic granulite metamorphism. A unique feature of zircon from the Khapchan gneisses is that its cores did not retain the age marks of the protolith, but were completely reset during metamorphism both in terms of the U-Pb system and the trace element composition, which can be explained by the extremely high intensity of fluid impact during the granulite facies metamorphism superimposed on the rocks of the Khapchan terrane of the Anabar Shield.