Aim: Fusobacterium nucleatum has gained attention in the endodontic literature as it is a predominant microorganism in primary, secondary, and persistent root canal infections. Current irrigants have lot of drawbacks and are unlikely to predictably achieve a bacteria-free root canal system, which can lead to these failures. Herbal alternatives are now gaining popularity in the field of endodontics, paving a new way in the disinfection of root canals. The aim of this study is to evaluate the antimicrobial efficacy of green tea extract and Triphala as root canal irrigants against F. nucleatum using real-time Polymerase chain reaction (PCR). Methods: Extracted teeth were taken and inoculated with F. nucleatum, which was grown in a Mueller–Hinton agar plate under anaerobic conditions. The samples were cleaned and shaped and irrigated with green tea extract, Triphala extract, and dimethyl sulfoxide, which were compared to the widely used irrigant, sodium hypochlorite. Cycle threshold value was used to calculate the efficacy of the irrigant against F. nucleatum after which the samples were subjected to reverse transcriptase PCR. The data were analyzed and the data between the group were compared using the one-way ANOVA followed by a post hoc Tukey’s test. Results: Triphala extract demonstrated high antimicrobial activity against F. nucleatum1. It revealed statistically significant differences between Triphala extract and sodium hypochlorite (NaOCL) (P = 0.001). Green tea extract also displayed antimicrobial activity. Both the Triphala and green tea extracts showed a significant difference (P < 0.001). Conclusion: Triphala extract showed better antibacterial efficacy when compared to 3% NaOCl and green tea extract against F. nucleatum.