<p>Drought is a natural calamity that occurs around the world when water supply falls drastically below normal levels in terms of precipitation and streamflows. The Upper Indus Basin (UIB) in Pakistan is a vital section of the Indus water tower, which is regrettably vulnerable owing to climate change. The current study calculates the drought severity index using the Standardized Precipitation Index (SPI) for the entire UIB, Jhelum River Basin (JRB) and Kabul River Basin (KRB). We observe the effect of El-Niño Southern Oscillation (ENSO) phases (El-Niño, La-Niña, and neutral) on SPI, consecutive dry days (CDD), and maximum precipitation (R20/R50). We use the Nino 3.4 index, Oceanic Niño Index (ONI) and ERA5 reanalysis gridded precipitation products from 1991 to 2020, with in-situ measurements from 1991 to 2017. To assess the significance of the observed trends, we applied the Innovative Trend Significance Test (ITST), which addresses serial correlation more robustly than conventional statistical methods. We observe a significant relationship between ENSO and SPI in all basins in 1998, 2003, and 2014, with maximum wetness occurring in 1999, 2000, 2010, and 2011 due to a strong La-Niña influence, although El-Niño enhances SPI in 1991, 1997, 2002, 2004, 2009, 2015, and 2016. ENSO phases strongly influence ERA5 SPI in the same regions. SPI and R20/R50 exhibit a general decline across most stations in the JRB (Bagh, Garhi Dupatta, Kallar, Khandar, Mangla, Murree, and Muzaffarabad), the KRB (Chitral, Dir, and Drosh), and the UIB (Gilgit and Gupis), although increasing trends are observed at a few stations within these basins. Meanwhile, CDD show a significant increase at several monsoon-dominated stations in the JRB, including Kallar, Murree, Mangla, and Muzaffarabad, whereas declining CDD trends are evident at Bagh, Balakot, and Parachinar. This study will contribute to an improved comprehension of precipitation droughts and extremes under ENSO influence.</p>