Background Study on the effect of hydroxychloroquine (HCQ) in treating children with chronic immune thrombocytopenia (ITP) is limited. The association between ANA positivity and its efficacy is not clear. Methods This was a retrospective cohort study on chronic ITP children. We compared the clinical characteristics of patients who received HCQ with those who didn’t, as well as patients who responded to HCQ at 3 months with those who didn’t. Mixed-effects models were performed to assess the effect of HCQ on platelet counts and the association between ANA and its efficacy. Records of side effects associated with HCQ were reviewed. Results A total of 191 children with chronic ITP were included in this study, involved 42 patients who received HCQ. In patients who received HCQ, 69.0% of patients achieved complete response /response at the last follow-up, with a higher frequency than in patients who didn’t (69.0% vs. 48.3%). The overall response rate was 56.8% at 3 months and 40.5% at 1 year. Our results showed no difference in ANA positivity between patients with response to HCQ and those without. HCQ was effective for increasing platelet counts (mean difference: 23.82×109/L; 95% CI: 7.44 ~ 40.21), but the association between ANA positivity and its efficacy was not found. Side effects were recorded in 6 of 42 patients (14.3%). Conclusions HCQ was associated with increased platelet counts in chronic ITP children. The baseline ANA level was not found to have an interaction effect on this efficacy. Side effects of HCQ should be concerned.