Objective To analyze the timing and mid-term prognosis of bypass surgery for children with Kawasaki disease complicated with coronary artery aneurysms. Methods A retrospective analysis was conducted on the clinical data of children with Kawasaki disease complicated with coronary artery aneurysms who underwent coronary artery bypass grafting at Shanghai Children's Medical Center affiliated to Shanghai Jiao Tong University School of Medicine from March 2018 to December 2023. Results Finally, 20 pediatric patients were enrolled, including 16 males and 4 females, with a median age of 118 (74, 140) months. All patients who failed drug treatment and had progressive coronary artery dilation with thrombosis underwent bypass surgery, including 14 patients with cardiac arrest and 6 patients without cardiac arrest. One patient died of severe left heart failure. The median follow-up of 19 surviving children was 34 (16, 61) months, and 84.2% of them had electrocardiogram recovery. The coronary artery diameter decreased from (16.2±9.2) mm to (8.2±2.7) mm, and the left ventricular ejection fraction increased from (58.2±8.6)% to (63.8±7.0)%. The 89.4% (17/19) of the patients’ vessels were unobstructed, and 94.7% (18/19) of the heart function recovered to grade Ⅰ/Ⅱ. Conclusion Coronary artery bypass grafting is safe and effective for treating Kawasaki disease coronary artery aneurysms in children, with a good mid-term prognosis.