Background: To determine the antibacterial effect of propolis nanoparticles (PNs) as an endodontic irrigant against Enterococcus faecalis biofilm in root canal. Methods: PNs were prepared by ultrasonication and the particle size distribution and polydispersity index were determined by dynamic light scattering using Zetasizer Nano S90. 210 extracted human teeth were sectioned to obtain 6mm of the middle third of the root. The root canal was enlarged to an internal diameter of 0.9mm. The specimens were inoculated with E. faecalis for 21 days. Following this, specimens were randomly divided into seven groups having 30 dentinal blocks in each group including group I: saline, group II: propolis 100µg/ml, group III: propolis 300µg/ml, group IV: propolis nanoparticle 100µg/ml, group V: propolis nanoparticle 300µg/ml, group VI: 6% sodium hypochlorite, group VII: 2% chlorhexidine. Dentine shavings were collected at 200 and 400 μm depths, and total numbers of CFUs were determined at the end of one, five, and ten minutes. The non-parametric Kruskal Wallis and Mann-Whitney tests were used to compare the differences in reduction of CFUs between all groups and probability values of P < 0.05 were set as the reference for statistically significant results. The scanning electron microscope and confocal laser scanning microscopy were also performed after exposure to PNs. Results: PN300 was significantly more effective in reducing CFUs compared to all other groups (p <0.05) except 6% NaOCl and 2% CHX (p >0.05) at all-time intervals and both depths. At five minutes, 6% NaOCl and 2 % CHX were the most effective in reducing CFUs (p <0.05) however, no significant difference was found in between PN300, 6% NaOCl and 2 % CHX at 10 minutes (p >0.05). SEM images also showed the maximum reduction of E. faecalis with PN300, 6% NaOCl and 2% CHX (>90 %) at five and ten minutes. CLSM images showed the number of dead cells in dentin was highest with PN300 (>90%) compared to PN100 (>40%) and saline (all live cells). Conclusion: PN300 was equally effective as 6% NaOCl, and 2% CHX in reducing E. faecalis CFUs after one minute, five and ten minutes at both depths.