Aim The present study aims to compare the antibacterial efficacy of a novel automated endodontic irrigation device with that of a manual irrigation technique. Materials and methods The present study considered 45 extracted single-rooted teeth. After sectioning the teeth, the specimens were inoculated with Enterococcus faecalis (E. faecalis) bacteria for three weeks. Instrumentation was done using ProTaper Gold rotary files to size 50 and 5% taper. Based on the irrigation protocol, the experimental samples were divided into Group I: control (normal saline irrigation) (n = 15); Group II: conventional needle irrigation (n = 15); and Group III: automated irrigation (n = 15). The irrigation in Group III was done using the automated irrigation device. After the experimental irrigation, the pre-weighted dentinal shaving was collected in Eppendorf tubes, diluted 10 times, and incubated in the Petri dish with tryptone soy agar (TSA) for 48 hours. Finally, the colony-forming unit (CFU) counts were assessed. IBM SPSS Statistics for Windows version 23.0 (Armonk, NY, USA, IBM Corp.) was used for data analysis. Intergroup comparisons were made using the non-parametric Kruskal-Wallis test. Results The mean CFU count (CFU/ml) for the groups was: Group 1 (normal saline irrigation): 3.67x101; Group 2 (manual irrigation): 2.69× 101; Group 3 (automated irrigation): 1.57× 101. A statistically significant reduction in E. faecalis CFU count was seen among the groups assessed (p<0.01). The automated irrigation group exhibited the most substantial reduction in E. faecalis CFU count. Group 2 showed a significant difference compared to Group 1 (p<0.05). Conclusions The novel automated endodontic irrigation device was superior to manual irrigation in reducing E. faecalis CFU counts. This indicates that the automated irrigation device has the potential to enhance bacterial elimination efficacy during endodontic treatment.