Lake Issyk-Kul occupies a large Late Mesozoic–Cenozoic intramontane basin between the mountain ranges of the Northern Kyrgyz Tien Shan. These ranges are often composed of granitoid basement that forms part of a complex mosaic assemblage of microcontinents and volcanic arcs. Several granites from the Terskey, Kungey, Trans-Ili and Zhetyzhol Ranges were dated with the zircon U/Pb method (SHRIMP, LA-ICP-MS) and yield concordant Late Ordovician–Silurian (~456–420Ma) emplacement ages. These constrain the “Caledonian” accretion history of the Northern Kyrgyz Tien Shan in the amalgamated Palaeo-Kazakhstan continent. The ancestral Tien Shan orogen assembled in the Early Permian when final closure of the Turkestan Ocean ensued collision of Palaeo-Kazakhstan and Tarim. A Late Palaeozoic structural basement fabric formed and Middle–Late Permian post-collisional magmatism added to crustal growth of the Tien Shan. Permo‐Triassic cooling (~300–220Ma) of the ancestral Tien Shan was unraveled using 40Ar/39Ar K-feldspar and titanite fission-track (FT) thermochronology on the Issyk-Kul granitoids. Apatite thermochronology (FT and U–Th–Sm/He) applied to the broader Issyk-Kul region elucidates the Meso-Cenozoic thermo-tectonic evolution and constrains several tectonic reactivation episodes in the Jurassic, Cretaceous and Cenozoic. Exhumation of the studied units occurred during a protracted period of intracontinental orogenesis, linked to far-field effects of Late Jurassic–Cretaceous accretion of peri-Gondwanan blocks from the Tethyan realm to Eurasian. Following a subsequent period of stability and peneplanation, incipient building of the modern Tien Shan orogen in Northern Kyrgyzstan started in the Oligocene according to our data. Intense basement cooling in distinct reactivated and fault-controlled sections of the Trans-Ili and Terskey Ranges finally pinpoint important Miocene–Pliocene (~22–5Ma) exhumation of the Issyk-Kul basement. Late Cenozoic formation of the Tien Shan is associated with ongoing indentation of India into Eurasia and is a quintessential driving force for the reactivation of the entire Central Asian Orogenic Belt.