Abstract. Poor reliability of radiosonde records across South Asia imposes serious challenges in understanding the structure of upper-tropospheric and lower-stratospheric (UTLS) region. The Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) mission launched in April 2006 has overcome many observational limitations inherent in conventional atmospheric sounding instruments. This study examines the interannual variability of UTLS temperature over the Ganges–Brahmaputra–Meghna (GBM) river basin in South Asia using monthly averaged COSMIC radio occultation (RO) data, together with two global reanalyses. Comparisons between August 2006 and December 2013 indicate that MERRA (Modern-Era Retrospective Analysis for Research Application) and ERA-Interim (European Centre for Medium-Range Weather Forecasts reanalysis) are warmer than COSMIC RO data by 2 °C between 200 and 50 hPa levels. These warm biases with respect to COSMIC RO data are found to be consistent over time. The UTLS temperature show considerable interannual variability from 2006 to 2013 in addition to warming (cooling) trends in the troposphere (stratosphere). The cold (warm) anomalies in the upper troposphere (tropopause region) are found to be associated with warm ENSO (El Niño–Southern Oscillation) phase, while quasi-biennial oscillation (QBO) is negatively (positively) correlated with temperature anomalies at 70 hPa (50 hPa) level. PCA (principal component analysis) decomposition of tropopause temperatures and heights over the basin indicate that ENSO accounts for 73 % of the interannual (non-seasonal) variability with a correlation of 0.77 with Niño3.4 index whereas the QBO explains about 10 % of the variability. The largest tropopause anomaly associated with ENSO occurs during the winter, when ENSO reaches its peak. The tropopause temperature (height) increased (decreased) by about 1.5 °C (300 m) during the last major El Niño event of 2009/2010. In general, we find decreasing (increasing) trend in tropopause temperature (height) between 2006 and 2013.