This paper presents an apatite U–Pb and geochemistry archive for exposed plutons and metamorphic rocks of the Kyrgyz South Tian Shan (STS) within the Central Asian Orogenic Belt. Apatite U–Pb dates and trace-element geochemistry are provided for 17 samples from late Carboniferous – early Permian I-type granites in the Terktinsky complex and A-type granites in the Kokshaal Range; early Devonian granites in the Kembel complex; Cryogenian granitoids and tuffs from the Middle Tian Shan and gneisses from the Atbashi metamorphic complex. These samples form a comprehensive selection of igneous and metamorphic rocks within the cores of Mesozoic basement highs that supplied detritus to adjacent basins such as the Tarim, Ferghana and Yarkand-Ferghana Basins. Generally, the granitoid samples preserve primary igneous apatite U–Pb ages that are within uncertainty of previously published zircon U–Pb dates. The apatites from the Atbashi metamorphic complex record anomalous Ordovician dates with large uncertainties that are interpreted as mixing ages between Cryogenian protolith formation and Carboniferous metamorphism. Principal component analysis discriminates apatite samples from the different bedrock terranes in the Kyrgyz STS based on their geochemical fingerprint and categorizes the samples with respect to an extensive apatite geochemical archive. The combined apatite-zircon archive provides a novel framework for provenance studies on the Meso–Cenozoic sedimentary history of the Central Asian Orogenic Belt.