Kawasaki disease (KD) is an acute, febrile, and systemic vasculitis that primarily occurs in infants and young children. Although the aetiology is unknown, it is considered that abnormal activation of monocytes/macrophages but not lymphocytes could occur during the acute phase of KD. Neutrophils may have a pivotal role in the pathogenesis of KD as well as the formation of coronary artery lesions (CAL). Primary autoimmune neutropenia (AIN) is a common form of chronic benign neutropenias of childhood. AIN, occuring in infancy, is characterised by persistent severe neutropenia (<500/μL of absolute neutrophil counts [ANC]), detection of the autoantibodies against neutrophil-specific antigens, and 95% of resolution before 4 years of age. There has been only one report on a patient with AIN who developed severe KD after the administration of granulocyte colony-stimulating factor. Here, we describe a 21-month-old female with AIN who developed full-blown KD on severe neutropenia remained. Single dose intravenous immunoglobulin led to a prompt response with defervescence. During the convalescent phase of KD, the patient showed a rapid increase and the following recovery of ANC in concert with the elevated levels of serum transforming growth factor-beta 1, that is one of the representative immunoregulatory cytokines. During hospitalization, echocardiography indicated no evidence of CAL. The pathophysiology of KD and the resolution of autoimmunity were discussed with special reference to the cytokine profiles.