The long‐term benefits of interferon‐α (IFN‐α) treatment in children with chronic hepatitis B (CHB) remain unclear. We conducted a retrospective and real‐world study to evaluate the safety and long‐term clearance rates of hepatitis B e antigen (HBeAg) and hepatitis B surface antigen (HBsAg) in CHB children who received IFN‐α monotherapy for 72 weeks and were with 13‐year follow‐up visit. Participants treated with IFN‐α (n = 316) were more likely to become HBeAg negatve (39.87% vs. 27.37%; p < .05) and HBsAg negative (11.08% vs. 3.16%; p < .05) by the end of the treatment period than untreated participants (n = 95). Treated participants also had higher cumulative rates of HBeAg loss (74.13% vs. 59.27%; p < .05) and HBsAg loss (46.95 vs. 33.11%; p < 0.05) than untreated participants in parallel by the end of 13‐year follow‐up. In particular, the cumulative rate of HBsAg loss was higher in treated children aged 1–7 years than in those aged 8–17 years (71.40% vs. 39.0%; p < .01). Children who were HBeAg‐negative at the end of IFN‐α treatment or who had serum alanine aminotransferase levels of ≥80 IU/L at baseline were likely to have higher cumulative HBsAg loss rates. Accordingly, HBeAg loss at 72 weeks was positively associated with the cumulative HBsAg loss rate in untreated children. There were no serious adverse events of IFN‐α therapy for the treated patients throughout the study period. Overall, IFN‐α therapy was effective in obtaining higher long‐term cumulative rates of HBeAg and HBsAg loss in children with HBeAg‐positive immune‐active CHB, especially among those aged 1–7 years.