Alanine aminotransferase (ALT) flare remains one of the determinants of initiating antiviral therapy in children with chronic hepatitis B (CHB). Insufficient data exist regarding children with CHB attributed to mother‐to‐child transmission. This study aimed to assess the occurrence of spontaneous ALT flares and identify factors affecting therapy‐induced hepatitis B surface antigen (HBsAg) loss in the flare cohort. We retrospectively included untreated children with mother‐to‐child transmitted CHB. The primary outcomes were spontaneous ALT flares and therapy‐induced HBsAg loss. Among 83 untreated children, 73.5% (61/83) experienced spontaneous ALT flares during the median follow‐up of 14.6 months (range, 0.1–177.1 months), with 54.1% of the first ALT flares and 44.3% of ALT peaks occurring within 6 years of age. Thirty‐six of 61 children with ALT flares received antiviral therapy, nine (25.0%) of whom achieved therapy‐induced HBsAg loss with a median duration of 19.3 months (range, 6.5–56.2 months). The age of initiation of antiviral therapy was the sole predictor of therapy‐induced HBsAg loss (HR = 0.544, 95% CI 0.353–0.838, p = 0.006). The restricted cubic spline showed a negative relationship between the age of initiation of antiviral therapy and HBsAg loss and identified that 6.2 years of age discriminated children with therapy‐induced HBsAg loss. Kaplan–Meier estimations suggested a higher probability of HBsAg loss in children who started antiviral therapy before 6.2 years old (p = 0.03). In conclusion, asymptomatic ALT flares were frequent in preschool‐aged children with mother‐to‐child transmitted CHB, and early initiation of antiviral therapy showed promising effects in those children with ALT flares.