Dental caries is a multifactorial disease which affects all age bar in different segments of society. With the burden of high-risk caries different approach have been advocated to manage the untreated lesions with affordable cost and noninvasive procedures. The aim of the study is to compare the antibacterial effect of silver diamine fluoride and sodium fluoride varnish. The colony forming units at baseline and after 3 days shows reduction in both the groups. Therefore, significant reduction was seen more in SDF compared to NaF group. After 6 months of reapplication of SDF and NaF varnish, the mean reduction seen in the S.mutans count was significant in both the groups. At the end of 6 months, when the intergroup significance was considered, significant reduction was observed in the group of subjects who received SDF application when compared to the group of subjects who received fluoride varnish. It was concluded that there is a reduction in the S. mutans count in both the groups after SDF and NaF application. SDF was shown to produce significant reduction. Due to the greater antibacterial efficacy of SDF, it can be used as an effective topical fluoride agent for caries prevention.