There is evidence that cardiorespiratory fitness and physical activity significantly reduce cardiovascular risks in adults. A better understanding of the association between cardiorespiratory fitness, physical activity, and childhood obesity is vital in assessing the benefits of interventions to prevent obesity. This study was to examine the relationship between physical activity, body mass index, and cardiorespiratory fitness levels in Taiwanese children. A cross-sectional study was designed. Study participants consisted of 2419 school children (1230 males and 1189 females) aged 12 years old living in a southern Taiwan county with one the highest countrywide rates of childhood obesity. The weight status of the participants was defined as underweight, normal, overweight, or obese according to specific criteria. Cardiorespiratory fitness was then assessed by an 800-m run. Participants were queried on their physical activity habits via a questionnaire survey. The overall prevalence of overweight/obesity was 29.6%. Normal, underweight and overweight boys and girls had an increased odds ratio of being categorized with higher cardiorespiratory fitness than obese one for both gender. A significantly higher level of cardiorespiratory fitness was found in children who engaged in regular physical activity than in children who engaged only in irregular physical activity. Obese children are more likely to lack cardiorespiratory fitness. Physically active children have significantly better cardiorespiratory fitness levels than inactive children. This study supports the conclusion that BMI and physical activity are significantly correlated with cardiorespiratory fitness levels. Findings may provide educational professionals with information to assist their developing effective health promotion programs to healthy weight and improving cardiorespiratory fitness for children.