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 ~19ka, with the peak water level of ~35m above the present elevation occurring at ~15ka. This was synchronous with a significant advance of the glacier in the catchment. Stepwise lake regression, including a rapid lowering of the lake level (~13m at ~12ka), persisted until at least ~10ka. Lake transgression and localized glacier expansion from ~19 to ~15ka 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.