It is known that children and adolescents with Kawasaki disease (KD) can maintain normal cardiopulmonary fitness (CPF) after the disease’s acute stage has subsided. This study aimed to investigate whether gender differences affect CPF in children and adolescents with KD. We retrospectively reviewed a cohort of 204 participants (120 boys and 84 girls) with KD. All participants were instructed to complete a symptom-limited cardiopulmonary exercise test (CPET) adapted to assess their CPF. Based on body mass index (BMI), boys and girls were categorized into groups of underweight (19 boys and 12 girls), normal (62 boys and 59 girls), and overweight (39 boys and 13 girls). Although a similarity in body composition was found among both genders for KD subjects and normal Taiwanese peers, the percentage of overweight subjects was higher in KD boys than the normal Taiwanese boys. When comparing CPF for different BMI groups, the whole KD group showed no discrepancy, but a significantly lower peak VO2 for the overweight KD boys group was observed, representing poorer CPF. In conclusion, girls with KD had better CPF than boys, and gender stereotypes affect sports participation as well as self-efficacy, and may be contributing to poorer CPF in KD boys.