Overall petrologic and geochemical data indicate that the early Paleozoic magmatism in the Olkhon area of the Baikal Region exhibits diverse types of granitoids, whose time of formation is estimated at a narrow age interval of 500–465 Ma. This magmatism was responsible for the formation of both autochthonous gneiss–migmatite–granitoid suites (Sharanur complex) and multiphase intrusions (Aya complex) emplaced into the upper horizons of the continental crust. In major-element chemistry, K2O/Na2O values, and rare-element composition the migmatite–plagiogranites and calc-alkaline and subalkaline granitoids of the Sharanur complex are similar to the host gneisses and schists, as they were likely derived from melting of the ancient metamorphic substratum of the Olkhon series. In new isotope-geochemical characteristics (ICP MS method) the Sharanur granitoids are close to the first-phase biotite granites of the Aya massif, whose further geochemical evolution was governed mainly by intrachamber magmatic differentiation leading to the production of second-phase leucogranites enriched in HREE and HFSE (in particular, Ta and Nb) and depleted in Sr, Ba, Eu, Li, and LREE. The origin of the autochthonous and intrusive granitoids is related to early Paleozoic collision events within the Olkhon metamorphic terrane, while the formation of syncollisional granitoids is best explained by both melting of the crust protolith (Sharanur complex) and magmatic differentiation (multiphase Aya intrusion). All mineralogical and geochemical characteristics indicate that these granitoids are distinguished from rare-metal pegmatoid granites and Li–F and Rb–Be–Nb pegmatites, whose vein bodies crosscut the granitoids, and are regarded as middle Paleozoic rocks, which mark the transition to within-plate magmatism in the Baikal Region.