This study investigated the disinfection efficacy of the upper-room ultraviolet germicidal irradiation (UR-UVGI) system with ceiling fans. The investigation used the steady-state computational fluid dynamics (CFD) simulations to solve the rotation of ceiling fan with a rotating reference frame. Two ambient air exchange rates, 2 and 6 air changes per hour (ACH), and four downward fan rotational speeds, 0, 80, 150 and 235 rpm were considered. In addition, the passive scalar concentration simulations incorporated ultraviolet (UV) dose by two methods: one based on the total exposure time and average UV fluence rate, and another based on SVE3* (New Scale for Ventilation Efficiency 3), originally defined to evaluate the mean age of the air from an air supply opening. Overall, the CFD results enabled the evaluation of UR-UVGI disinfection efficacy using different indices, including the fraction of remaining microorganisms, equivalent air exchange rate, UR-UVGI effectiveness and tuberculosis infection probability by the Wells–Riley equation. The results indicated that air exchange rate was the decisive factor for determining UR-UVGI performance in disinfecting indoor air. Using a ceiling fan could also improve the performance in general. Furthermore, the results clarified the mechanism for the ceiling fan to influence UR-UVGI disinfection efficacy.