Kawasaki disease (KD) is characterized by acute systemic vasculitis and frequently is complicated by coronary artery lesions (CALs). The inositol 1,4,5-trisphosphate 3-kinase C (ITPKC) gene rs28493229 was recently found to be associated with the risk for KD in the Japanese population, suggesting that the ITPKC gene may contribute to KD susceptibility. This study investigated the association of ITPKC polymorphisms with KD in a Han Chinese population. Five ITPKC Single-nucleotide polymorphisms, including rs28493229, were genotyped in 223 unrelated patients who had KD and 318 non-KD control subjects. The allele, genotype, and haplotype frequencies were compared between the patients and the control subjects, between the patients with and those without CALs, and between patients resistant to intravenous immunoglobulin treatment and those responsive to such treatment. Multiple alleles were observed for rs28493229 and rs2290692. No significant differences in the frequencies of the C allele, the CC genotype, or the C carriers of rs28493229 were observed in the comparisons. Interestingly, significantly higher frequencies of the C allele (p < 0.001), the CC genotype (p = 0.001), and the C carriers (p = 0.003) were observed for rs2290692 among the patients than among the control subjects, and similar differences were observed between the patients with and those without CALs. The GC haplotype for rs28493229 and rs2290692 was more common among the patients than among the control subjects. The results indicate that the C allele of the ITPKC gene rs2290692 is linked to a significantly higher risk for KD in the studied population, which provides new evidence to support the importance of the ITPKC gene in the occurrence of KD. More notably, this finding suggests that there may be an unidentified ITPKC polymorphism in strong linkage disequilibrium to rs2290692, significantly affecting susceptibility to KD in the Han population.