The source region of the Indus River (SRIR), which is located in the Hindukush, Karakoram and Himalayan (HKH) mountainous range and on the Third Pole (TP), is very sensitive to climate change, especially precipitation changes, because of its multifarious orography and fragile ecosystem. Climate changes in the SRIR also have important impacts on social and economic development, as well as on the ecosystems of the downstream irrigation areas in Pakistan. This paper investigates the changes in precipitation characteristics by dividing the daily precipitation rate into different classes, such as light (0–10 mm), moderate (10.1–25 mm) and heavy precipitation (>25 mm). Daily precipitation data from gauging and non-gauging stations from 1961–2015 are used. The results of the analysis of the annual precipitation and rainy day trends show significant (p < 0.05) increases and decreases, respectively, while light and heavy precipitation show significant decreasing and increasing trends, respectively. The analysis of the precipitation characteristics shows that light precipitation has the highest number of rainy days compared to moderate or heavy precipitation. The analysis of the seasonal precipitation trends shows that only 18 stations have significant increasing trends in winter precipitation, while 27 stations have significant increasing trends in summer precipitation. Both short and long droughts exhibit increasing trends, which indicates that the Indus Basin will suffer from water shortages for agriculture. The results of this study could help policymakers cope with floods and droughts and sustain eco-environmental resources in the study area.