Long‐term hydroclimate change can provide reliable reference for water resources management in Central Asia. However, only a few palaeohydrological records exist in Tajikistan. To obtain a long‐term perspective on hydrological changes in Tajikistan, we developed, for the first time, a streamflow reconstruction from September of the previous year to June of the current one in the Kafirnigan River basin, based on Juniperus semiglobosa tree‐ring width indices from the Iskanderkul area in northern Tajikistan. The streamflow reconstruction explains 40% of the actual streamflow variance during the period 1939–1993. Spatial correlation analyses with gridded precipitation data indicate that our streamflow reconstruction contains a strong regional hydroclimatic signal for southern Central Asia. The high and low intervals of our streamflow reconstruction are closely related to the interdecadal variations of El Niño‐Southern Oscillation (ENSO). Our reconstructed streamflow is significantly correlated with sea surface temperatures in the eastern equatorial Pacific Ocean and northern Indian Ocean, indicate the existence of remarkable 11‐, 5.6–5.7‐, 4.3‐, 2.6‐, 2.3‐ and 2.0‐year cycles, and suggest a relationship between southern Central Asian streamflow variations and ENSO activity.