Background The dose of methylprednisolone therapy for intravenous immunoglobulin-resistant Kawasaki disease (IVIG-resistant KD) remains controversial. The study aims to investigate the effect of low-dose intravenous methylprednisolone (IVMP) therapy on children with IVIG-resistant KD. Methods 36 IVIG-resistant KD children were recruited. Coronary artery lesions (CAL) were recorded before these children were first treated with IVIG. 15 patients were treated with a second course of IVIG (2 g/kg/dose) after unsuccessful treatment with IVIG (2 g/kg/dose), named IVIG group. 21 patients with IVIG-resistant KD were treated with a second course of IVIG and low-dose IVMP (2 mg/kg/day) for 3-5 days after unsuccessful treatment with IVIG, named IVIG+IVMP group, including 8 patients with CAL and 13 patients without CAL. The level of brain natriuretic peptide (BNP) in serum was detected by electrochemiluminescence immunoassay. Results The treatment was successful in 21 (100%) of the patients who received additional IVIG along with IVMP and 10 (66.7%) who received additional IVIG. In IVIG+IVMP group, BNP decreased significantly after patients received additional IVIG along with IVMP. 72h After treated with additional IVIG and IVMP, there was no difference of BNP levels between patients with CAL and without CAL in IVIG+IVMP group. None of the patients was with CAL followed up for 1 year in IVIG+IVMP group.Conclusion This study suggest that low-dose IVMP along with additional IVIG is an effective treatment for IVIG-resistant KD, and low-dose IVMP increases no risk of CAL.