The India-Asia collision, which started about 50 Ma ago, resulted not only in mountain building in the Himalayas. Recently about 50% of the total India-Asia convergence is accommodated in the Tian Shan orogenic system, far “behind” the collision zone. The start of uplift of the Tian Shan ranges is strongly debated. Most estimations, based on thermochronology, range from Oligocene to Late Miocene. The intermontane Ili Basin in southeastern Kazakhstan accommodates continuously clastic continental sediments since the Paleogene, recording the uplift history of the Tian Shan mountains. The basin is subdivided by young basement uplifts, providing good outcrops of the basin fill. The study of numerous sections revealed growth strata and progressive unconformities in different stratigraphic levels, specific for particular basement anticlines. First indications of deformation were observed already in late Eocene units. Uplift of basement anticlines and activity of thrust faults was interrupted by periods of tectonic quiescence and continuous deposition. Alluvial fan progradation documents uplift in the hinterland. Large alluvial fans were active during different periods, some disappeared and became reactivated. The basin fill documents asynchrony of growth strata, unconformities and alluvial fan progradation, proving spatially and temporally differentiated tectonic uplift throughout the Ili Basin. We explain the varying activity of structures by strain partitioning at major strike-slip faults or temporary locking of thrusts by the load of the hanging wall, possibly caused by low erosion rates during arid climate.