We developed a novel, compact upper‐room ultraviolet germicidal irradiation system with light‐emitting diode sources (UR‐UVGI‐LED) to enhance the disinfection of bioaerosols in an enclosed room space. Its effectiveness was evaluated and compared with the conventional upper‐room ultraviolet germicidal irradiation system with mercury vapor sources (UR‐UVGI‐MV). Escherichia coli, Serratia marcescens, and Staphylococcus epidermidis were atomized under the well‐mixed condition and exposed to UR‐UVGI‐LED (or UR‐UVGI‐MV) device. The intensity output of the UR‐UVGI‐LED was also varied from 0% (no LED), 25%, 50% to 100% to further evaluate the UR‐UVGI‐LED disinfection effectiveness under different power levels. The decay rates for UR‐UVGI‐LED ranged from −0.1420 ± 0.04 min⁻¹ to −0.3331 ± 0.07 min⁻¹ for Escherichia coli, −0.1288 ± 0.01 min⁻¹ to −0.3583 ± 0.02 min⁻¹ for Serratia marcescens, and −0.0330 ± 0.01 min⁻¹ to −0.0487 ± 0.01 min⁻¹ for Staphylococcus epidermidis. It was noticed that the intensity level had a non‐linear influence on the UR‐UVGI‐LED’s performance. The decay rates achieved by the UR‐UVGI‐MV system were −0.3867 ± 0.08 min⁻¹, −0.4745 ± 0.002 min⁻¹, and −0.1624 ± 0.02 min⁻¹ for Escherichia coli, Serratia marcescens, and Staphylococcus epidermidis, respectively. Hence, the disinfection performance of both UR‐UVGI‐LED and UR‐UVGI‐MV systems was comparable for Escherichia coli and Serratia marcescens. These results demonstrate that the UR‐UVGI‐LED system has a high potential to be used as a safe and effective irradiated light source to disinfect indoor airborne pathogens.