There are no robust data from clinical trials to guide the clinician in the choice of therapeutic agents for the child with intravenous immunoglobulin (IVIG) resistance. Moreover, the treatment regimen for IVIG-resistant patients varies between institutions, and the best option has not yet been established. Therefore, in this trial, 955 patients with Kawasaki disease (KD) were selected and were initially treated with IVIG (2 g/kg), of these patients, 80 (8.38%) assessed as IVIG resistant were randomly divided into two groups: Group A (n = 40) received a second IVIG treatment, and Group B (n = 40) received methylprednisolone pulse therapy (MPT). Duration of fever, duration of fever after retreatment, hospital days, medical costs, readmission rate, and laboratory examination difference (△) were calculated. Coronary artery lesions (CALs) outcomes were followed up over two years. Patients in MPT group had a shorter fever after retreatment and lower medical costs; more rapid decline in C-reactive protein (CRP), Neutrophils% (N%), platelets (PLT) levels; and a more rapid rise in sodium. However, they also had a higher incidence of treatment failure and CALs than the additional IVIG treatment group in the long-term follow-up. Caution is still required in the use of MPT to treat IVIG-resistant KD.