There is a host of literature on the subject from many authors but I'll surmise the problem: schools reward behaviour like being quiet and attentive in class, sitting still for longer periods, not goofing off and following instructions which is far more common in girls than it is in boys while punishing typically 'boyish' behaviour (which more or less comes down to the opposite of the former). Outdoors and practical activities - which are more aligned to the way boys learn - are limited to a minimum or even taken away completely while indoors, formal classroom-based teaching based on literacy and numeracy is the norm, an environment tailored to those aforementioned traits which are more common in girls. Boys do better when they have positive male role models but male (and here it is important to realise I'm not just talking about sex but also about behaviour, i.e. 'typically male') teachers and assistants are as rare as hen's teeth in the primary and increasingly also in the secondary school systems. Continuous assessment plays a larger role in setting final results, again favouring girls as they are essentially being rewarded for having the earlier characteristics while boys are being punished for lacking them. In some school systems - the Swedish being one of them according to the teacher's union - girls get higher test scores than boys for the same performance when the tests are scored by the pupil's teachers [1]. A study titled "Grading and gender : Equality or discrimination?" [2] arrives at similar conclusions.

[1] https://lararnastidning.se/pojkar-missgynnas-i-betygsattning...

[2] http://kth.diva-portal.org/smash/record.jsf?pid=diva2%3A1205...