Periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome is the most commonly encountered autoinflammatory disease in children, but its pathogenesis and diagnostic biomarkers are unknown. In this study, we examined the utility of CD64, a member of the Fcγ receptors, expressions on neutrophils and monocytes in diagnosing patients with PFAPA, along with other autoinflammatory diseases exhibiting periodic fever, and bacterial infections. Although CD64 was expressed at a similar level in the attack-free period of PFAPA and in controls, CD64 expressions on both neutrophils and monocytes were dramatically increased during attacks. Serum IFN-γ also increased in some PFAPA patients during flares, suggesting the involvement of T cell activation. Our findings demonstrate that remarkable CD64 expression during PFAPA flares serves as a potential biomarker for the diagnosis. We also suspect that IFN-γ, possibly from retention of activated T cells in peripheral tissues, increases CD64 synthesis in such cases.