Objectives: Infected root canals contain resistant bacteria with high resistance to antibacterial solutions such as Enterococcus faecalis (E. faecalis). Therefore, this study was aimed to evaluate and compare the antibacterial effect of the chitosan (CH) and Diode laser on an infected root canal. Subjects and Methods: Four disinfectant systems were used in the present study; 2.5% sodium hypochlorite (NaOCl) "control group", 0.2% chitosan solution, low-level diode laser (1.5-watt), and chitosan/diode laser in combination. This study involved a total of sixty-four carious primary molar teeth indicated for pulpectomy in children aged between 4-7 years. Results: All disinfectant systems showed a statistically significant effect against E. faecalis. There was a statistically significant difference between the four tested systems, while among the groups, there is no statistically difference between NaOCl and diode laser, and between diode laser and combination of chitosan/diode laser. Conclusion: The use of chitosan and laser alone or in combination has a significant effect on the reduction of E. faecalis count. However, the use of diode laser and combination of chitosan/diode laser as disinfectant systems showed a statistically comparable result to NaOCl.