The aim of this study was to determine the relationship among obesity, physical activity level, physical fitness and academic performance among female secondary school students in Shah Alam. Two hundred and fourteen participants (age: 16 years, body height: 156.76 ± 5.65 cm, body mass 59.92 ± 13.35 kg, BMI: 24.41 ± 5.00 kg/m2) participated in this study. Students with a body mass index above 25 kg/m2 were classified as obese. Physical activity level was evaluated by using International Physical Activity Questionnaire (IPAQ), while physical fitness was evaluated by the total score of four fitness components (cardiovascular endurance, muscular endurance, muscular strength, flexibility) measured by SEGAK used in Malaysia secondary schools. Academic performance was assessed by the Average School Grade (ASG) from the Form Three Assessment (PT3) results of the previous year. There was a negative significant relationship between obesity and physical activity level (r = -0.20, p < 0.05), obesity and physical fitness (r = -0.42, p < 0.05), obesity and academic performance (r = 0.49, p < 0.05), physical activity level and physical fitness (r = 0.54, p < 0.05), physical activity level and academic performance (r = -0.14, p < 0.05). and physical fitness and academic performance (r = -0.26, p < 0.05). These results suggested that obesity status, physical activity level and physical fitness could not only affect health status but also academic performance in secondary school students.