Dental caries is one of the most prevalent chronic diseases among preschool children globally. Different preventive agents and combinations have been studied. However, the rank of the effectiveness of clinical interventions is equivocal. To summarize and rank the effectiveness of clinical interventions using different agents for primary prevention of early childhood caries (ECC). Two reviewers independently searched PubMed, Embase, and Cochrane Library to identify randomized controlled trials with at least 12-month follow-up. The network meta-analysis (NMA) on different agents was based on a random-effects model and frequentist approach. Standardized mean differences (SMD) with 95% CI of the caries increment were calculated in terms of either dmft or dmfs and used in the NMA. Caries incidences at the child level were compared using odds ratios (ORs) with 95% CI. The effectiveness of the agents was ranked using the surface under the cumulative ranking curve (SUCRA). After screening 3807 publications and selection, the NMA finally included 33 trials. These trials used either a single or combination of agents such as fluorides, chlorhexidine, casein phosphopeptide-amorphous calcium phosphate, probiotics, xylitol, and triclosan. Compared with control, fluoride foam (FF; SMD -0.69, 95% CI: -1.06, -0.32) and fluoride salt (F salt; SMD -0.66, 95% CI: -1.20, -0.13) were effective in preventing caries increment. Probiotic milk plus low fluoride toothpaste (PMLFTP; OR 0.34, 95% CI: 0.15, 0.77), FF (OR 0.48, 95% CI: 0.37, 0.63), fluoride varnish (FV; OR 0.63, 95% CI: 0.48, 0.81), and fluoride varnish plus high fluoride toothpaste (FVHFTP; OR 0.73, 95% CI: 0.57, 0.93) were effectively preventing caries incidence. According to the SUCRA, FF ranked first in preventing caries increment, whereas PMLFTP ranked first in preventing caries incidence. Fluoride foam, F salt, PMLFTP, FV, and FVHFTP all effectively reduce caries increment or caries incidence in preschool children, but the evidence indicates low degree of certainty. Considering the relatively small number of studies, confidence in the findings, and limitations in the study, clinical practitioners and readers should exercise caution when interpreting the NMA results.