Purpose: Although the diagnosis of Kawasaki Disease (KD) is made based on clinical signs, laboratory parameters associated with inflammation are supportive in the diagnosis of incomplete KD. This study aimed to analyse laboratory values according to fever duration, and evaluate the relationship across laboratory indices during the acute phase of KD to aid in the early diagnosis for early-presenting incomplete KD patients. Methods: This was a retrospective cohort study of patients diagnosed and treated for KD at two university hospitals in Daejeon, Korea (n = 615). The patients’ clinical and laboratory findings were reviewed. Initial laboratory indices were evaluated according to the duration of fever at presentation. Clinical and laboratory data between the patients with coronary artery lesions (CALS) and those without CALs were analysed. Also, the relationships across laboratory indices were evaluated using the patient group with fever duration of 5 days and 6 days (n = 204). Results: The mean age was 29.7 ± 21.4 months, and male-to-female ratio was 1.6:1. The mean fever duration was 6.6 ± 2.3 days, and the proportions of patients with CALs was 19.3% (n = 114); of which 8 had aneurysms. The C-reactive proteins (CRP) and neutrophil differential levels were highest in patients presenting on the sixth day, whereas haemoglobin, albumin, and lymphocyte differentials were lowest on the sixth day. Compared to patients with CALs vs. those without CALs, the total fever duration (7.4 vs. 6.4 days, p = 0.001) was longer, and the rate of repeated intravenous immunoglobulin administration (IVIG) (18.5% vs. 7.5%, p = 0.01) was higher. Also, the mean CRP value was higher (11.6 vs. 9.0 mg/dL, p = 0.001), and the mean values of haemoglobin (10.9 vs. 11.2 g/dL, p = 0.001) and albumin (3.5 vs. 3.7 g/dL, p = 0.001) were lower in the CALs groups compared to the patients without CALs. Among laboratory indices, the values of CRP, albumin, neutrophil differential, and haemoglobin at peak inflammation stage of KD were statistically correlated positively or negatively each other. Conclusions: The severity of systemic inflammation was reflected by laboratory values including CRP, neutrophil differential, albumin and haemoglobin. Observing changes in these laboratory parameters prior to IVIG treatment may aid in the early diagnosis of early-presenting KD patients.