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Background To study the caries lesion activity response to topical 38% silver diamine fluoride (SDF) therapy with increasing treatment application time. Methods/design The design is a stratified-randomised, double-blind, active-controlled, parallel-group clinical trial with nine treatment arms. The trial will involve recruiting at least 414 3- to 5-year-old kindergarten children with caries, who will receive approximately 0.004 mL of 38% SDF (the typical amount applied per the manufacturer’s instructions) to treat each caries lesion. The children will be stratified by caries status, randomised by blocks, and allocated to nine groups of SDF application times: 3, 5, 10, 15, 30, 45, 60, 120, and 180 s. The outcome measure is caries lesion activity (active/arrest) at the tooth-surface level at 6 months post-initial treatment. A calibrated dentist will conduct the blinded clinical examinations at baseline and at the 6-month follow-up. In addition, the parents will be surveyed to examine the effects of the moderating variables, such as oral hygiene, on caries lesion activity. The hypothesis is that a monotonically increasing trend can be found between the SDF application time and the proportion of caries lesions that are arrested. The Cochran-Armitage test for trends in proportions, corrected for clustering within children, will be used to determine the relationship between the exposure to SDF (the SDF application time) and the response (proportion of lesions arrested) in children, taking into consideration the effect of the moderating variables as well as the nesting of multiple caries lesions within an individual child. An EC 80 analysis (an 80% maximal concentration) will be used to determine the exposure (the SDF application time) for 80% caries lesion arrest. Bootstrap methods will be used for clustered data and will be resampled by clustering to determine the 95% confidence interval. Discussion This study will help with determining the optimal application time for SDF treatment. It will provide an evidence-based protocol for the use of SDF to arrest tooth decay in the primary teeth of young children. The results will inform an evidence-based SDF protocol to arrest caries, which affects 573 million children with tooth decay worldwide. Trial registration ClinicalTrials.gov NCT04655430. Registered on 7th December 2020.