Objectives Physical inactivity and poor physical fitness in children and adolescents are growing public health problems globally. This study aimed to investigate the correlation between Body Mass Index (BMI) and three physical fitness components, including overall fitness, according to the Swedish Physical power, Mental harmony and Social capacity profile (FMS profile). Another aim was to investigate the test-retest reliability of the FMS questionnaire and fitness tests. Methods A total of 3,692 male and female adolescents in Sweden, between year 2004 and 2013, aged from 16 to 18 years old, were included. Height and weight data were collected to calculate the Body mass index (BMI). The participants performed physical fitness tests, which measure cardio-respiratory fitness, muscular strength and flexibility. The test-retest study included 18 adolescents, aged 16. They answered the FMS questionnaire and participated in the fitness tests with one-week interval. Results A weak inverse relationship between BMI and physical fitness was found: r=−0.06 to −0.07 (p<0.05) for flexibility, r=−0.13 to 0.10 (p<0.001) for strength, r=−0.14 to −0.33 (p<0.001) for cardiorespiratory fitness, and r=−0.15 to −0.27 (p<0.001) for overall fitness. In the test-retest study, the ICC’s for strength, flexibility and balance were 0.94, 0.96 and 0.89, respectively. The ICC’s for the questions regarding lifestyle ranged from 0.75 to 1.00 and for diet, physical activity and drugs were 0.56, 0.44 and 0.58, respectively. The correlation was stronger in overweight/obese individuals compared to normal weight individuals. Conclusion Overweight and obese individuals scored lower in the fitness tests compared to their normal weight counterparts. The test-retest study revealed that the FMS questionnaire and fitness tests are reliable tools.