Although effective preventive strategies exist for pit and fissure caries, prevention of proximal caries remains a significant challenge. This split-mouth study was designed to investigate the effect of glass-ionomer cement (GIC) on the progression of initial proximal caries in posterior teeth, testing the hypothesis that local application of fluoride-releasing GIC would reduce this progression. GIC was applied to 41 pairs of posterior teeth after elastic band separation in 7- to 19-year-old individuals. Follow-up bitewing radiographs were taken at 6 and 12 months. Differences in Δ mean lesion depth at 6 and 12 months between test and control groups were significant (p < 0.05, p < 0.000). Lesions treated with GIC were more likely to remain in or regress to the outer half of enamel (OR = 6.3; 95%CI, 1.3-30.9). GIC provides an effective approach to the clinical management of incipient proximal caries.