Irrigation has significant role in endodontic treatment, many types of antimicrobial irrigation solutions have been used, but due to the ineffectiveness, safety concerns and side effects of this irrigation, the herbal alternatives for endodontic irrigants might be beneficial. Objectives This study compared the in vitro effectiveness of tea tree oil and clove oil as possible irrigants in endodontics against Enterococcus faecalis in comparison with 3% Sodium hypochlorite. Materials and Methods E. faecalis was isolated from patients in need for endodontic treatment; VITEK was employed for E. faecalis isolate conformation. Muller Hinton agar was prepared with 100μl of freshly prepared suspension of E.faecalis. Wells of 6mm diameter and 4mm depth were punched in each petri dish, the well were filled with 50 μl of: Group I: 3% sodium hypochlorite, Group II: 50% clove oil, Group III: 100% clove oil, Group IV: 100% tea tree oil. All petri dishes were incubated at 37oC for 24hr Zone of inhibition of the bacterial growth was calculated Results Statistical analysis of the obtained results was calculated. One way ANOVA was performed among four groups which showed as highly statistical difference with a p-value <0.01, LSD test was performed, group I & group IV is significantly was higher than group II, group III (p-value = 0.001), while there were no significant differences between group I & group IV (p-value = 0.165). Conclusion Both tea tree oil &clove oil showed antimicrobial activity against Enterococcus faecalis, however, tea tree oil & Sodium hypochlorite had better antimicrobial properties than clove oil.