Introduction The goal of endodontic therapy is to completely eliminate the infection and stop microbes from infecting or reinfecting the root canal and the periradicular tissues. Amongst the primary microorganisms, Enterococcus faecalis (E. faecalis), a Gram-positive anaerobe, is the main cause of pulpal and periapical inflammation causing root canal failure. Literature evidence shows that the gold-standard calcium hydroxide is ineffective against E. faecalis due to its resistance to the alkaline pH and proton pump mechanism. Herbal essential oils such as oregano, basil, and thyme are known to possess antimicrobial properties against E. faecalis. However, their combination with calcium hydroxide as an intracanal medicament and the depth of penetration is still unknown. Aim To evaluate the depth of penetration of calcium hydroxide mixed with three different herbal essential oils using a confocal laser scanning microscope. Material and methods Fifty single-rooted premolars were decoronated and randomly divided into five groups. Group 1 - Oregano oil with calcium hydroxide, Group 2 - Basil oil with Calcium hydroxide, Group 3 - Thyme oil with calcium hydroxide, Group 4 - Calcium hydroxide with saline, Group 5 - Negative control. The teeth were instrumented and inoculated with E. faecalis and incubated for 21 days. Calcium hydroxide mixed with respective oils or saline and 0.1% rhodamine B dye was placed in the canals and again incubated for 7 days. Two sections each of 1 mm were horizontally cut at 3 mm and 5 mm from the apex and later subjected to a confocal laser scanning microscope to evaluate the depth of penetration. One-way ANOVA, post-hoc Tukey test, and student t-test were performed. Results At the middle third, basil oil had the maximum depth of penetration (1377.47±14.1 µm) followed by oregano oil (1345.4±26.5 µm) and thyme oil (1160.4±24.6 µm). At apical third, basil oil (1152.4±31.6 µm) showed maximum depth of penetration, followed by thyme (988.3±26.2 µm) and oregano oils (419.5±19.8 µm). The depth of penetration of these oils was greater at the middle third than at the apical third. Conclusion Basil, oregano, and thyme oil have good penetration depth into the dentinal tubules and can be successfully used in root canal procedures as intracanal medicaments.