Clinical features and laboratory parameters in patients with incomplete Kawasaki disease (KD) and systemic juvenile idiopathic arthritis (s-JIA) tend to overlap. Furthermore, there have been no definite biomarkers for these diseases. This situation makes the clinical diagnosis of these patients difficult. In this study, we aimed to measure serum interleukin (IL)-18 and IL-6 levels in patients with s-JIA who were initially diagnosed with incomplete KD and compare these data with those in patients with complete KD and arthritis. Serum IL-18 levels in patients with s-JIA were significantly elevated compared with those in patients with KD and arthritis. Pediatricians should be aware that the presentation of s-JIA can mimic incomplete KD. Because the clinical features overlap, a high index of suspicion is warranted. The measurement of serum IL-18 may be useful for differentiating s-JIA from KD.