Operational faults are common in the heating, ventilating, and air conditioning (HVAC) systems of existing buildings, leading to a decrease in energy efficiency and occupant comfort. Various fault detection and diagnostic methods have been developed to identify and analyze HVAC operational faults at the component or subsystem level. However, current methods lack a holistic approach to predicting the overall impacts of faults at the building level—an approach that adequately addresses the coupling between various operational components, the synchronized effect between simultaneous faults, and the dynamic nature of fault severity. This study introduces the novel development of a fault-modeling feature in EnergyPlus which fills in the knowledge gap left by previous studies. This paper presents the design and implementation of the new feature in EnergyPlus and discusses in detail the fault-modeling challenges faced. The new fault-modeling feature enables EnergyPlus to quantify the impacts of faults on building energy use and occupant comfort, thus supporting the decision making of timely fault corrections. Including actual building operational faults in energy models also improves the accuracy of the baseline model, which is critical in the measurement and verification of retrofit or commissioning projects. As an example, EnergyPlus version 8.6 was used to investigate the impacts of a number of typical operational faults in an office building across several U.S. climate zones. The results demonstrate that the faults have significant impacts on building energy performance as well as on occupant thermal comfort. Finally, the paper introduces future development plans for EnergyPlus fault-modeling capability.