BACKGROUND Streptococcus mutans is considered as the main pathogenic factor for initiation and progression of dental caries. Fluoride is one of the most effective agents used to control caries. Chlorhexidine (CHX) is the most antimicrobial agent against S. mutans and dental caries. OBJECTIVE The study aimed to compare the effectiveness of antimicrobial activity of CHX-thymol (CHX/T) and fluoride varnishes on S. mutans levels in children's saliva aged from 6 to 8 years old. METHODS The total number of children involved in this study is sixty, ages 6 and 8 years old. The participants were divided into three groups by block randomization: Group 1 CHX/T varnish, Group 2 fluoride varnish (f varnish, and Group 3 control group. Varnish was applied onto all tooth surfaces of the participants. At the baseline conditions, saliva samples were collected from the participants for bacterial examination test. This procedure was repeated in week 1, 4, and 12. Bacterial quantitative test was performed, and the number of S. mutans was estimated. RESULTS The results revealed the significant efficacy of the two groups (fluoride and CHX/T varnishes) in reducing salivary S. mutans numbers when compared to the control group (P < 0.05). In terms of salivary colony-forming unit counts reduction of S. mutans, no significant difference was observed between the fluoride and CHX/T varnish groups (P > 0.05). CONCLUSIONS The outcomes showed that there was a significant reduction in S. mutans counts in children's saliva following the application of fluoride and CHX/T varnishes.