The changes to the hydrological cycle as a consequence of climate change significantly affect the water security of countries worldwide. The Brahmaputra Basin (BB), a biodiversity hotspot, is among the world's wettest regions and is vulnerable to climate change. Using ground and satellite-based datasets from multiple sources and a percentile-based analysis from 1998 to 2018, it is found that an asymmetric trend exists in extreme rainfall over the hills and the adjacent plains of the basin. The hills experience a decline in rainfall, whereas, over the plains, an increase is observed on similar rainfall days. During 1998-2018, mean accumulated rainfall over the whole basin declined by as much as ∼60% during the October to December (OND) period. Similarly, a decline of ∼20% is observed for June to September (JJAS). The most significant reduction in mean rainfall was mainly over the wettest regions of the basin, such as Cherrapunji/Mawsynram and is concentrated in the highest percentile (extreme events) of rainfall distribution. Such an overall decline in total rainfall coupled with altitudinal asymmetry in percentile distributions of rainfall may contribute towards flood hazards with changing lead time for warning, posing severe socio-economic challenges.