The link between lithosphere thinning and formation of world-class gold deposits is well established in the Jiaodong Peninsula within the eastern North China Craton (NCC). However, the timing of initiation and duration of the lithospheric thinning process as well as the depth of formation of the mineralization remain uncertain. Since these parameters are fundamental to formulate exploration strategies, in this study we perform fission track (FT) analysis on zircon and apatite grains in Late Mesozoic granitoid samples from the Jiaodong Peninsula and provide new constraints for the mode and duration of lithospheric evolution and mineralization depth. The zircon FT ages range from 64.3 to 90.9 Ma and those of apatite show a range of 32.8–50.9 Ma. The data collectively display age peaks at ~60–80 and ~30–50 Ma. Reverse modelling of the apatite FT results indicates rapid crustal uplift during ~30–80 Ma in the Jiaodong Peninsula. This period coincides with the timing of maximal sedimentation in the neighboring basins and voluminous basaltic eruptions in the eastern NCC. We suggest that the Jiaodong Peninsula has experienced two stages of crust uplift in the Late Cretaceous and Paleogene as a consequence of the continuing lithosphere thinning, together with the surrounding basins, forming the horst–graben system in the eastern NCC. The Late Mesozoic granitoids are the main wall rocks for gold deposits in Jiaodong, and thus the crust denudation history gathered from the FT data suggest that the gold mineralization formed at depths of c. 6–11 km.