Dental caries is the most common chronic childhood disease. Products of metabolism by bacteria populating the tooth surface induce development and progression of cavities. We sought to determine whether a polyvinylpyrrolidone-iodine (PVP-I; povidone-iodine) and NaF topical varnish was superior to one containing only NaF in prevention of new dental caries lesions in a single-center randomized active-controlled trial based on a double-blind, parallel-group design. The site was Pohnpei State, Federated States of Micronesia. The study population was healthy children 49 to 84 mo old who were enrolled in early childhood education: 284 were randomized (1:1 allocation), and 273 were included in year 1 analysis and 262 in year 2. The test varnish contained 10% PVP-I and 5.0% NaF. The comparator contained only 5.0% NaF but was otherwise identical. Varnishes were applied every 3 mo during 2 y. The primary outcome was the surface-level primary molar caries lesion increment (d2-4mfs) at 2 y. Caries lesion increments from baseline to year 1 and year 2 were compared between conditions with log-linear regression, adjusting for age and sex and whether the tooth was sound at baseline (free of caries lesions). At year 1, the caries lesion increment for primary molars sound at baseline was 0.9 surfaces (SD = 1.5) for the test varnish versus 1.8 (SD = 2.2) for the comparator varnish with fluoride alone (adjusted rate ratio, 0.50; 95% CI, 0.31 to 0.81; P = .005). At year 2, the caries lesion increment for primary molars sound at baseline was 2.3 surfaces (SD = 2.8) for the test varnish as compared with 3.3 (SD = 2.7) for the comparator (adjusted rate ratio, 0.74; 95% CI, 0.52 to 1.03; P = .073). Teeth that were already cavitated at baseline did not show a preventive effect. There were no harms. A dental varnish containing PVP-I and NaF is effective in the primary prevention of cavities in the primary dentition (NCT03082196). This study demonstrates that periodic application of a varnish containing NaF and PVP-I is effective in prevention of caries lesions and useful in assessing the potential of combined treatment.