We report a 3-year-old boy with giant and atypical coronary artery aneurysms in the acute phase of Kawasaki disease, despite appropriate therapeutic intervention, in Noonan syndrome with a novel heterozygous PTPN11 mutation, c. 907 G>A (p.Asp303Asn). We hypothesised that this PTPN11 mutation might affect both hyperinflammation caused by Kawasaki disease and vascular fragility in the coronary artery, resulting in coronary artery aneurysms.