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Background: Evidence for the benefit of applying Fluoride Varnish FV to permanent teeth is generally very positive. However, the caries-inhibiting effect of FVs on primary teeth is still debatable. Aim: To assess the effectiveness of fluoride varnish in prevention of early childhood caries in children over the period of 3 years in high fluoride areas. Study design: A double-blind cluster-randomized controlled trial was undertaken amongst 3-4 years old children. The varnish application was done at three points in the intervention group. Results: Experimental group showed significantly lesser increment in mean ICDAS score than control group at both 12 month and 36 months. Preventive fraction was 72.4% at 12 months and 18.2% at 36 months. Multiple linear regression showed that at 12 months, intervention was the significant predictor with varnish group having 0.140 (95% CI 0.175–0.230) lower net caries increment. At 36 months, baseline ICDAS score and intervention were the significant predictors. Conclusion: This study suggests that fluoride varnish is an effective and a safe mode of prevention of early childhood caries in children residing in high fluoride zone. However, the overall effect is influenced by the baseline caries status.