The lake-level variations during the Late Glacial in the Lake Karakul basin (a closed glacierized-basin), in the northernmost part of the eastern Pamirs, were reconstructed using geomorphological and sedimentological evidence, with a chronology developed using luminescence ages from sand-sized quartz and K-feldspar in the lake sediments. Lake transgression started before ~ 19 ka, with the peak water level of ~ 35 m above the present elevation occurring at ~ 15 ka. This was synchronous with a significant advance of the glacier in the catchment. Stepwise lake regression, including a rapid lowering of the lake level (~ 13 m at ~ 12 ka), persisted until at least ~ 10 ka. Lake transgression and localized glacier expansion from ~ 19 to ~ 15 ka likely correlate with the more regional Late Glacial glacier advances across the semi-arid western Himalayan–Tibetan orogen and the eastern Pamirs. The longer-term trend of this lake transgression was probably caused by colder and/or wetter climatic conditions, forcing a notable glacier advance.