Background. Use of herbal compounds as an intracanal medicament in the field of endodontics has become noteworthy, one of which is the Aloe vera compound whose antibacterial effect has already been proven in the planktonic form of Enterococcus faecalis. The purpose of this study is to evaluate the antibacterial effect of Aloe vera on E. faecalis biofilms at the 4th and 6th week of development. Materials and Methods. 130 single root canal teeth without anomalies and caries were used. They were divided into two groups of 65 teeth for four and six weeks of biofilm production. Five samples of each group were examined for confirmation of biofilm formation under an electron microscope. Study groups were investigated with an antimicrobial agent as an intracanal medicament including 20 samples treated with Aloe vera, calcium hydroxide, and phosphate-buffered saline, and biofilm and survival of pathogens were investigated. Dentin chip suspensions were used for colony-forming unit (CFU) counting to estimate remaining E. faecalis counts. Results. The CFU mean in the 4th week subgroup in Aloe vera, phosphate-buffered saline, and calcium hydroxide was 0, 69166.66 ± 31688.58, and 25000 ± 30822.07, and in the 6th week, it was 136.36 ± 323.33, 95000 ± 12247.44, and 27501.66 ± 36570.34, respectively, which showed a significant difference between the used materials (
p
<
0.05
). Conclusion. Aloe vera, in contrast to calcium hydroxide, eliminated 4th and 6th week biofilms and showed remarkable antibacterial properties against E. faecalis biofilm. These results support potency of Aloe vera to use as a natural antimicrobial material in the intracanal medicament.