The primary objective of this clinical trial was to assess the caries-preventive efficacy of 2 years of twice weekly supervised brushing with a self-applied gel containing 12,500 ppm fluoride on schooldays compared with weekly supervised use in children at high caries risk (with prior caries experience on first permanent molars). The secondary objective was to assess efficacy compared with similar children who continued with their usual oral hygiene care. This was a single-centre, single-blind, randomised, parallel-groups trial comprising two test groups and one untreated control group. 1,075 pupils aged 12–13 years at baseline received a baseline and final examination 2 years later. For all children completing the trial no significant difference was found between groups. For children compliant with study protocol no significant difference was found in the primary outcome (D1FS caries increment), but significant differences were found between the three groups overall in the secondary outcome, D3FT caries increment, with a significant pairwise difference between control and twice per week gel brushing (29%, p = 0.023 D3FT visual + fibre-optic transillumination). Analysis of the relationship between number of gel applications and caries showed that children who brushed with the gel at least 60 times over a 2-year period developed significantly fewer carious lesions into dentine than children who followed their usual oral hygiene routine. Some caution is needed as greatest benefit was shown by compliant children. Where schools are co-operative, it is recommended that the gel be used twice a week within a school-based programme over a 2-year period.