A meta-analysis was performed on published data on the caries-inhibiting effect of fluoride gel treatment in 6- to 15-year-old children. The purposes of this meta-analysis were: (1) to calculate the overall caries-inhibiting effect of clinical fluoride gel treatment studies, based on explicit selection criteria, and (2) to explore factors potentially modifying the effect of fluoride gel treatment in caries prevention, concerning the baseline caries prevalence of the target population, the general fluoride regimen, and application features. The caries-inhibiting effect of fluoride gel application was assessed by the prevented fraction and the ‘number needed to treat’. The overal prevented fraction of the fluoride gel treatment studies, indicating the reduction of caries incidence by fluoride gel treatment relative to the incidence in the control group, was 22% (95% CI = 18–25%). Multiple regression analysis showed no significant influence on the prevented fractions for the variables ‘baseline caries prevalence’, ‘general fluoride regimen’, ‘application method’, and ‘application frequency’. The ‘number needed to treat’ (NNT), indicating the number of patients that need to be treated in order to prevent 1 DMFS, estimated the efficiency of fluoride gel treatment according to the caries incidence of the target population, including cost/effect relations. It was found that the NNT = 18 in a population with caries incidence 0.25 DMFS per year, and NNT = 3 in a population with caries incidence = 1.5 DMFS per year (treatment duration 1 year). From the standpoint of cost-effectiveness, the additional effect of fluoride gel treatment in current low and even moderate caries incidence child populations must be questioned.