Multiple cardiovascular sequelae have been reported late after Kawasaki disease (KD), especially in patients with coronary artery lesions. In this perspective, we hypothesized that exercise response was altered after KD in patients with coronary aneurysms (CAA-KD) compared to those without history of coronary aneurysms (NS-KD). This study is a post hoc analysis of exercise data from an international multicenter trial. A group of 133 CAA-KD subjects was compared to a group of 117 NS-KD subjects. Subjects underwent a Bruce treadmill test followed to maximal exertion. Heart rate (HR), systolic blood pressure (SBP), and diastolic blood pressure (DBP) were assessed at each stage of the test including recovery. Myocardial perfusion was evaluated by stress and rest Tc-99m sestamibi SPECT imaging. Endurance time was similar between NS-KD and CAA-KD (11.3 ± 2.6 vs. 11.0 ± 2.6 min; p = 0.343). HR, SBP, and DBP responses to exercise were similar between groups (p = 0.075–0.942). Myocardial perfusion defects were present in 16.5 % CAA-KD versus 22.2 % NS-KD (p = 0.255). Analysis based on myocardial perfusion status identified a lower heart rate at 1 min into recovery as well as lower DBP at 1 and 5 min into recovery in patients with abnormal SPECT imaging (p = 0.017–0.042). Compared to patients without CA involvement, the presence of coronary aneurysms at the subacute phase of KD does not induce a differential effect on exercise parameters. In contrast, exercise-induced myocardial perfusion defect late after the onset of KD correlates with abnormal recovery parameters.