Early childhood caries, a serious health problem among young children, can be prevented with effective intervention. The aim of this study was to evaluate the efficacy of oral health education and a fluoride varnish in the prevention of caries in children under the age of 3 years. For this single-blind randomized parallel group 1-year clinical trial in Shiraz, 300 children aged 12-24 months with sound primary teeth were selected and randomly divided into three groups (n = 100): (1) control: no preventive intervention; (2) oral health counseling, and (3) oral health counseling and fluoride varnish at baseline and 6 months later. At baseline and 4, 8 and 12 months after the intervention, caries risk reduction was recorded as the primary outcome. The mothers' knowledge and performance regarding oral health in children was used as a secondary outcome. A total of 260 children (mean age: 20.49 ± 7.33 months) completed the study. Compared to group 1, caries risk reduction in group 2 was 28% (95% CI: -39.05 to -17.45) and 31% in group 3 (95% CI: -41.88 to -21.73). However, there was no significant difference between groups 2 and 3 (95% CI: -8.58 to 1.47). In all groups, mothers' knowledge and performance at baseline were low; however, they increased significantly in follow-up appointments in groups 2 and 3 (p < 0.001). Oral health education increased mothers' knowledge and performance regarding oral health in children. Oral health counseling alone or associated with the use of fluoride varnish reduced the caries incidence in young children.