Watershed prioritization is essential in sub-watershed (SW) natural resource management. The Swat River watershed in the Hindukush mountains of Pakistan's Khyber Pakhtunkhwa province covers an area of 5337 km². Using an Advanced Spaceborne Thermal Emission and Reflection Radiometer digital elevation model with a resolution of 30 m obtained from the United States Geological Survey (USGS), the present study identified 17 SWs (SW1–17) with drainage patterns ranging from dendritic to sub-dendritic. The SWs were assessed for their susceptibility to erosion via GIS-based assessment using a morphometry-based compound factor (CF) approach. A total of 15 linear, aerial, and relief morphometric characteristics were identified and analyzed. The SWs were ranked for each morphometric parameter based on their contribution to the erodibility of the SW. A ranking of 1 indicated that the SW had the greatest susceptibility to erosion for that parameter and a ranking of 17 indicates that it had the lowest. These rankings were summed to calculate the CF, which thus indicated the combined influence of these characteristics on the erosion susceptibility of the SW (a lower CF indicated a higher susceptibility to erosion). The SWs were consequently divided into four groups based on their susceptibility to erosion using the calculated CF: very high, high, moderate, and low susceptibility. SW8, SW12, and SW15 had the lowest CFs (8.0, 8.9, and 8.9, respectively) and were thus extremely vulnerable to erosion. In contrast, SW1, SW2, and SW4 had the highest CFs (13.4, 13.8, and 11.8, respectively) and were the least vulnerable to erosion. The very high-priority SWs were characterized by the presence of fifth-order streams, a length of the overland flow of 1.20–1.61, a very high basin relief of 1720–2937, the highest relief ratio of 102.10–205.24, a low shape factor of 1.51–2.67, and a farm factor of 0.37–0.66. The present study demonstrates that the key morphometric characteristics that impact soil erosion are basin form and relief parameters, such as the basin relief and relief ratio. This study illustrates that the CF approach to determining the susceptibility of SWs to soil erosion is extremely valuable for planners and decision-makers for soil conservation efforts at the SW level.