ObjectivesTo compare the clinical efficacies of 5 % sodium fluoride varnish (NaFV) and glass-ionomer sealant (GIS) in preventing occlusal caries in primary second molars (PSMs). Materials and MethodsA total of 736 children were recruited from 18 kindergartens and randomised into either Group 1- receiving NaFV quarterly, or Group 2 - single placement of GIS at baseline. Interventions were performed on 1431 and 1264 PSMs in Group 1 and Group 2, respectively. The primary outcome was the development of ICDAS≥4 dentine caries at the occlusal surfaces of PSMs. ResultsA total of 736 children (383 in Group 1; 353 in Group 2) received the intervention. After 18–24 months, 479 children with 1764 PSMs were reviewed. Despite a low GIS retention rate of 2.4 % by 18–24 months, only 17.1 % of PSM in the GIS group developed caries into dentine. No significant difference was identified when compared to the proportion of PSMs with caries into dentine in the NaFV group (17.0 %). Regression analysis with GEE revealed that only baseline dft score and plaque level had a significant influence on development of ICDAS≥4 dentine caries in PSMs. ConclusionsQuarterly-applied NaFV and a single placement of medium viscosity GIS have similar clinical efficacies in preventing occlusal caries among preschool children. Clinical SignificanceThere is no significant difference between quarterly-applied NaFV and GIS in preventing occlusal caries at PSMs. Dental clinicians can choose to use either of these preventive methods after considering their own and parents’ preferences, children's cooperation and other practical factors.