Most of the leakage in water distribution systems operating with plastic pipes occurs at service connections (SCs), while the existing tools plan rehabilitation of pipes. With limited water resources, intermittent supplies in arid regions further enhance the failure vulnerability of metal fittings on water mains due to scale formation and large pressure transients. The present research developed a risk-based methodology for the proactive maintenance of SCs in intermittent water supply systems. A five-generation bottom-up hierarchical approach aggregated the basic hydraulic, physical, and water quality factors to determine the vulnerability of structural failures of SCs. Hydraulic parameters (pressure and velocity) were estimated by simulating a distribution network of 366 water mains of diameters ranging from 110 mm to 225 mm serving 371 SCs in a residential neighborhood located in the Qassim region of Saudi Arabia. Age, depth, and length of SCs’ estimated the condition index, while soil corrosivity and condition of the water mains were also counted when assessing the structural failure index for each SC. Water quality parameters, e.g., pH, turbidity, and iron, that can contribute to the vulnerability of an SC’s failure were also included. Fuzzy-based methods first assessed the relative importance weights of the basic input parameters at the bottom of the hierarchy and the risk factors in the middle of the hierarchy. Subsequently, the performance and condition scores were aggregated to develop respective indices. As the consequence of structural failure is high for the SCs serving households with a large number of residents, the final risk index aggregates the vulnerability and consequence at the hierarchy’s top. The developed model was effectively validated by comparing the SCs of high priority with the leaking and repaired SCs in the past. The method will be a useful tool for planning proactive inspection and rehabilitation of SCs of intermittent supply systems to minimize water losses (less than 8% of the national benchmark) in Saudi Arabia and elsewhere.