This study assessed the antibacterial activity of BioRoot RCS in comparison with that of the Totalfill BC and AH Plus sealers against Enterococcus faecalis biofilms in dentinal tubules using confocal laser-scanning microscopy. Sixty-six root dentin halves were prepared and sterilized. Three sections were used to ensure sterilization. The remaining were inoculated with E. faecalis. Three specimens were examined to verify the viability of biofilms. The sixty specimens were randomly divided into four groups: AH Plus, BioRoot RCS, Totalfill BC sealer, and no sealer. The specimens were incubated for 1, 7, and 30days. The specimens were stained and four corners of each disc were scanned. Statistical analysis was performed using two-way ANOVA and Tukey's post hoc test. Almost half of the bacteria were dead in BioRoot RCS group on day 1 and in Totalfill BC group on day 7. All sealers killed significantly more bacteria than the control after 30 days (P < .05). On day 7, Totalfill BC showed a significantly higher percentage of dead bacteria than BioRoot RCS (P < .05). On day 30, the BioRoot RCS group registered the highest percentage of dead cells (61.75%), which was significantly higher than the percentages of the AH Plus and Totalfill BC groups (P < .05). Calcium silicate-based root canal sealers exerted antimicrobial effects against E. faecalis biofilms. The antibacterial activity of BioRoot RCS was significantly higher than that of the Totalfill BC and AH Plus sealers after 30 days of exposure.