ObjectivesPhysical activity may be important in deterring the obesity epidemic. This study aimed to determine whether objectively measured physical activity in first year of upper secondary high school predicted changes in body composition over 2 years of follow-up in a cohort of Norwegian adolescents (n=431).DesignA longitudinal study of adolescents (mean age of 16 (SD 0.4) at baseline, 60.3% girls) participating in the Fit Futures studies 1 (2010–2011) and 2 (2012–2013).SettingAll eight upper secondary high schools in two municipalities in Northern Norway.ParticipantsStudents participating in both studies and under the age of 18 at baseline and with valid measurement of physical activity at baseline and body composition in both surveys.Primary and secondary outcomesChange in objectively measured body mass index and waist circumference and change in dual-energy X-ray absorptiometry measured fat mass index, lean mass index (LMI) and appendicular LMI (aLMI) between baseline and follow-up.ResultsAt baseline, boys had significantly higher physical activity volume (p=0.01) and spent on average of 6.4 (95% CI 2.1 to 10.6) more minutes in moderate-to-vigorous physical activity (MVPA) than girls (p<0.01). In girls, multivariate regression analyses showed that more sedentary time was negatively associated with changes in LMI (p<0.01) and aLMI (p<0.05), whereas more light activity had opposite effects on these measures (p<0.01 and p<0.05, respectively). No significant associations between measures of baseline physical activity and changes in body composition parameters were observed in boys.ConclusionsIn this cohort of Norwegian adolescents, sedentary and light physical activity was associated with changes in LMI and aLMI in girls, but not boys. Minutes spent in MVPA in first year of upper secondary high school was not associated with changes in measures of body composition in neither sex after 2 years.