Introduction: This study aimed at determining the association between cardiovascular fitness and physical activity with obesity and  changes in their patterns  among 12-16 year-old boys.  Materials and Methods: In this cross-sectional study, 275 boy students, 12-16 year-old from Bardaskan city were investigated. Subjects were selected via random sampling. Underweight, overweight and obesity status were evaluated based on the 5th, 85th and 95th percentiles of body mass index (BMI) for age and sex based on the United States’ Center for Disease Control (CDC 2000) standards. Physical activity levels were estimated by the Physical Activity Questionnaire for Older Children (PAQ-C). Cardiovascular fitness (VO2max) was assessed by a 20 m shuttle run test. Results: Overall prevalences of underweight, overweight and obesity among subjects were 3/6%, 10/5% and 4/7% respectively. There was significant positive correlation between physical activity level and  cardiovascular fitness. Cardiovascular fitness and physical activity levels decreased sign­ificantly with aging. The overweight and obesity groups had lower levels of cardiovascular fitness than the normal and underweight groups. There was no statistically significant difference between the overweight-obese and the non overweight groups in physical activity levels. Moreover, There was a significant negative correlation between physical activity and cardiov­ascular  fitness levels and subjects’ BMIs. Conclusion: Considering the in adequate levels of cardiovascular fitness and physical activity in overweight and obese boys, programs increasing physical activity (endurance exercise), and diet and weight control are recomme­nded for these groups.