The Ediacaran peralkaline granites, which were emplaced during the post-collisional tectonic extensional stage, have a limited occurrence in the northern tip of the Nubian Shield. In this contribution, we present new mineralogical and geochemical data of Mount El-Sibai granites from the Central Eastern Desert of Egypt. The aim is to discuss their crystallization condition, tectonic setting, and petrogenesis as well as the magmatic evolution of their associated mineralization. Mount El-Sibai consists of alkali-feldspar granites (AFGs) as a main rock unit with scattered and small occurrences of alkali-amphibole granites (AAGs) at the periphery. The AAG contain columbite, nioboaeschynite, zircon and thorite as important rare metal-bearing minerals. Geochemically, both of AFG and AAG exhibit a highly evolved nature with a typical peralkaline composition (A/CNK = 0.82–0.97) and formed in within-plate anorogenic setting associated with crustal extension and/or rifting. They are enriched in some LILEs (Rb, K, and Th) and HFSEs (Ta, Pb, Zr, and Y), but strongly depleted in Ba, Sr, P and Ti with pronounced negative Eu anomalies (Eu/Eu* = 0.07–0.34), consistent with an A-type granite geochemical signature. The calculated T_Zrn (774–878 °C) temperatures indicate that the magma was significantly hot, promoting the saturation of zircon. The texture and chemistry of minerals suggest that they were crystallized directly from a granitic magma and were later subject to late- to post-magmatic fluids. Both granitic types were most likely generated through partial melting of a juvenile crustal source followed by magmatic fractionation. The lithospheric delamination is the main mechanism which causes uplifting of the asthenospheric melts and hence provides enough heat for crustal melting. The produced parent magma was subjected to prolonged fractional crystallization to produce the different types of Mount El-Sibai granites at different shallow crustal levels. During magma fractionation, the post-magmatic fluids (especially fluorine) contribute significantly to the formation of rare metal mineralization within Mount El-Sibai granites.