Kawasaki Disease (KD) is a systemic vasculitis that can lead to coronary artery aneurysms (CAA) in up to 10% of treated cases, significantly increasing the risk of thrombosis and acute myocardial infarction (AMI). While thrombolytic therapy is commonly used in adult coronary syndromes, its application in pediatric KD remains poorly studied. We report a 9-month-old infant with KD and giant CAA complicated by a subocclusive thrombus in the left anterior descending artery (LAD). Initial systemic intravenous thrombolysis (IVCT) with alteplase failed to prevent progression to ST-elevation myocardial infarction (STEMI). Intracoronary thrombolysis (ICT) was subsequently performed, achieving partial reperfusion without complications. At 18 months of follow-up, the patient remained asymptomatic with stable left ventricular dysfunction. This single case illustrates the potential feasibility of combining ICT and IVCT in managing coronary thrombosis in pediatric KD. However, as a single observation, these findings cannot be generalized, and the approach requires further investigation. Robust multicenter studies are necessary to establish the safety, efficacy, and optimal use of thrombolytic therapy in pediatric KD patients with coronary thrombosis.