Aim: To evaluate and compare the antibacterial efficacy of 6% citric acid versus chitosan irrigant solution against Enterococcus Faecalis bacteria in treatment of root canals of primary anterior teeth Subjects and Methods: This in-vivo study was carried out on thirty anterior primary teeth of children attending the outpatient clinic of Pediatric Dentistry and Dental public health department Faculty of oral and dental Medicine, South Valley University. Ranging from three to six years of age. The teeth were equally divided into six groups (5 teeth each), based on the irrigant used during chemo mechanical preparation of the root canals. Results: There was a significance difference between the action of 6% chitosan and 6% citric acid against Enterococcus faecalis. Chitosan as root canal irrigation showed a significant antimicrobial effect. Citric acid as root canal irrigation has a lower antimicrobial effect when compared to chitosan and NaOCl. The 1% NaOCl as root canal irrigation has a higher antimicrobial effect. Conclusion: The use of 6% chitosan exhibited a comparable result to 1% NaOCl clinically and microbiologically.