Researchers also found that pupils doing an extra hour of daily homework and reading performed significantly better than their peers.
However, the level of physical activity had no effect on academic performance.
To look at the relationship between physical activity, sedentary behaviours and academic achievement, researchers led by the Medical Research Council (MRC) Epidemiology Unit at the University of Cambridge studied 845 pupils from secondary schools, measuring levels of activity and sedentary behaviour at age 14.5 years and then comparing this to their performance in their General Certificate of Secondary Education (GCSE) the following year.
Additionally the researchers used self-reported measures to assess screen time (the time spent watching TV, using the internet and playing computer games) and time spent doing homework, and reading for pleasure.
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The team found that screen time was associated with total GCSE points achieved.
Each additional hour per day of time spent in front of the TV or online at age 14.5 years was associated with 9.3 fewer GCSE points at age 16 years - the equivalent to two grades in one subject (for example from a B to a D) or one grade in each of two subjects, for example.
Screen time and time spent reading or doing homework were independently associated with academic performance, suggesting that even if participants do a lot of reading and homework, watching TV or online activity still damages their academic performance.
The researchers found no significant association between moderate to vigorous physical activity and academic performance, though this contradicts a recent study which found a beneficial effect in some academic subjects.
Although watching TV, playing computer games or being online were all associated with poorer grades, TV viewing was found to be the most detrimental.
The researchers found that those who spent their sedentary time doing homework or reading scored better at GCSE.
Pupils doing an extra hour of daily homework and reading achieved on average 23.1 more GCSE points than their peers.
The study was published in the International Journal of Behavioural Nutrition and Physical Activity.