The Pamir indentor of the northwestern Himalayan syntaxis is a first‐order feature demonstrating partly the northward extent of deformation due to the Cenozoic Indo‐Eurasia collision. The Alai Valley of Kyrgyzstan at the northern end of the indentor is a strategically positioned, E‐W trending intramontane basin that constrains the timing and extent of crustal deformation in this area of the collision zone. To quantify the convergence accommodated across the Alai Valley during the Late Cenozoic, we collected structural and stratigraphic field data, reviewed existing Soviet literature, and analyzed migrated seismic reflection profiles to construct and restore two regional sections crosscutting the basin. Our study suggests that the development, progressive closure, and conversion of this formerly marine basin into a terrestrial intramontane basin result from two main deformation events: (1) Distributed north‐south contraction took place during the late Oligocene–early Miocene, accommodated one third to half of the total shortening and was followed by the formation of a regional erosion surface; and (2) N‐S shortening resumed in the mid‐Miocene and continues today. During this second episode the thrust front migrated southward, localized along the Trans Alai ranges, and failed to reactivate earlier Neogene structures. Horizontal shortening of about 35% across the Alai Valley implies relatively low strain rates and displacement rates of about 4.18–4.69 × 10−16 s−1 and 0.66–0.78 mm yr−1, respectively, for the last 25 Myr. Our study confirms other regional observations indicating that contractional deformation occurred far in the interior of the Asian continent as early as the late Oligocene.

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