On average, the 14-year-olds said they spent four hours of their leisure time each day watching TV or in front of a computer.
The researchers found an additional hour of screen-time each day was associated with 9.3 fewer GCSE points at 16 - the equivalent of dropping a grade in two subjects.
Two extra hours of screen-time was associated with 18 fewer points - or dropping a grade in four subjects.
Pupils who put in an extra hour of homework or spent the time reading, did better in their GCSEs, scoring 23 points more than the average.
But even if pupils spent more time studying, more time spent watching TV or online, still harmed their results, the analysis suggested.
Extra time on moderate to vigorous physical activity had no effect on academic achievements.