Rainfall is very crucial component of hydrological cycle, which is major and primary source of the runoff. Runoff modelling is immensely beneficial for analysing, regulating and monitoring the quality and quantity of water resources. Determining surface runoff in a watershed is according to rainfall rate and quantifying discharge at outlet are critical in hydrological research. In this study, the HEC-HMS hydrological model version 10 was implemented for simulating the process of rainfall runoff in the Juba watershed of South Sudan. The satellite-derived precipitation data utilised in the study was obtained from NASA’s Integrated Multi-satellite Retrievals for Global Precipitation Measurement (GPM IMERG), for two years, 2021 and 2022. Methods such as Initial Constant, SCS Unit hydrograph and Muskingum routing were chosen to compute loss, transform method and flow routing, for the basin model, respectively. The research assisted in recognising different subbasin-level variations based on outflow from the rainfall through land use and land cover classes and DEM elevation values, which would be helpful in projecting and identifying different disasters and predicting the measures to tackle the disasters upcoming in the region.