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The least well-documented intramountain basin within the Tien Shan is the Fergana Basin. Cenozoic deformation is localized along thrusts on the northern and southern flanks, and by transpressive deformation associated with the dextral Talas–Fergana Fault on the eastern margin. We use sedimentological and stratigraphic observations from well-exposed Cenozoic outcrops to describe depositional environments, provenance and sources. These results are combined with interpreted seismic reflection lines and geological cross-sections are extended laterally based on outcrop geology to the north and east. Following a tectonically quiet early Cenozoic period, a progressive change in palaeocurrent indicators suggests Oligo-Miocene uplift of the hinterland, coupled with an increase in higher energy facies in the Massaget Formation. A renewed pulse of deformation tilted Massaget strata and deposited a considerable volume of coarse sedimentary rocks (Baktriy Formation). The younger episode moved progressively basinwards, as imaged by growth–strata relationships in the subsurface. Published work shows that the accumulation of an impressive c. 8 km of Cenozoic deposits cannot be accommodated only by lithospheric flexure produced by a tectonic load. We agree with the hypothesis that the thick sediments preserved in the basin are accommodated by lithospheric folding and propose that this is driven by compression associated with south-vergent Pamir subduction.

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