Purpose: The caries-preventive effect of pit and fissure sealant was found to be related to the incidence of caries in the population. The rate of caries in China has been very low, and a pit and fissure sealant public health programme has been widely carried out since 2005. This study aims to evaluate the caries-preventive effect of this dental public health programme in Beijing, the capital of China. Materials and Methods: A 3-year longitudinal study was conducted from 2012 to 2015. All students (n = 2973) in one district of Beijing were included. Children who received a sealant were categorised into the sealant group (n = 1648), and the other children were categorised into the no sealant group (n = 1325). Results: The dental caries risk levels in the sealant group and the no sealant group were balanced at baseline. The caries incidences of children only counting four first molars after 28 months were 18.1% and 13.6% for the sealant group and the no sealant group, respectively (Chi-square test, p = 0.001). The risk ratio in the sealant group versus the no sealant group for caries yes/no (only four molars) at 28 months was 0.73 (95% CI, 0.60–0.90; p = 0.001), based on binary logistic regression. Conclusions: The pit and fissure sealant dental public health programme implemented in Beijing was effective in preventing dental caries in the first permanent molars. Keywords: caries, prevention, programme evaluation, sealant(s)