Cost-effective and safe air disinfection methods are urgently needed in various environmental public settings. A novel UVC-based disinfection system was designed and tested to provide a promising solution because of its effective inactivation of indoor bioaerosols at a low cost. UVC light-emitting diodes (UVC-LEDs) were utilized as the irradiation source. This system has the unique feature of rotating the UVC-LEDs to generate a “scanning irradiation” zone. Escherichia coli was aerosolized into an experimental chamber, exposed to UVC-LEDs, and sampled using an impactor. Effects of air mixing (well-mixed vs. poorly-mixed), transmission range (short vs. long), and irradiation mode (stationary vs. rotating) were evaluated. The system performs significantly well under the poorly-mixed condition. The results obtained from the short disinfection range indicate that the rotating UVC was approximately 70.5 % more effective than the stationary UVC for the poorly-mixed case. Further, we evaluated the performance of the long disinfection range under a poorly-mixed situation, and the disinfection efficacy was 84.6 % higher for the rotating irradiation than that of the stationary. About 0.59–1.34 J/m² UV dose can be used to obtain one-log inactivation of E. coli. In conclusion, the novel rotating upper-room UVC-LED system is effective in reducing indoor pathogen transmission, and our findings are highly significant to a growing field where LEDs are applied for disinfection.