This multicenter double-blind randomized controlled trial aimed to determine the efficacy of daily or triweekly consumption of reconstituted milk powder, containing Lactobacillus paracaseiSD1, in preschool children for caries prevention. A 6-month intervention was conducted in 487 children (aged 37.6 ± 9.2 months) with ≤4 decayed teeth from 8 childcare centers. Using stratified block randomization, participants were randomly allocated into 3 groups, comprising: (1) daily probiotic, receiving probiotic milk once daily, (2) triweekly probiotic, randomly receiving probiotic milk 3 days a week and the placebo milk for the remaining 4 days, and (3) placebo, receiving milk without probiotics. Each tooth surface was assessed for caries status using the modified Nyvad criteria at baseline (T0), 6 (T6) and 12 (T12) months after T0. Study outcomes were caries transition, including caries progression and regression during the T0–T6, T6–T12 and T0–T12 periods. Negative binomial regression with a generalized linear model was used to estimate the caries outcomes, which were reported as incidence rate ratios (IRRs) and 95% confidence intervals (CIs). At baseline, caries prevalence and mean decayed surfaces were 81.9% and 7.29 ± 7.60, respectively. Three groups were balanced at baseline with an overall dropout rate of 25.2%. After adjusting for age, sex, and the number of noncavitated and cavitated caries at baseline, a decreased caries risk during T0–T6 was shown in both the daily and triweekly probiotic groups (adjusted IRR 0.83, 95% CI 0.72–0.96 in both groups) and during T0–T12 (adjusted IRR 0.84, 95% CI 0.76–0.94, and adjusted IRR 0.86, 95% CI 0.76–0.96, respectively) compared to the placebo group. In contrast, significantly increased regressive surfaces were demonstrated during T0–T6 by adjusted IRR 1.76 (95% CI 1.25–2.48) and 2.01 (95% CI 1.42–2.85) and during T0–T12 by adjusted IRR 1.98 (95% CI 1.50–2.61) and 1.92 (95% CI 1.45–2.55) for the daily and triweekly groups, respectively. In conclusion, probiotic milk consumption either daily or triweekly can modestly prevent new caries, but considerably reverse carious lesions, suggesting that a daily or triweekly dose interval is sufficient to reverse carious lesions.