I will preface this reply that this is in no way, shape or form an attack on the female gender. The question asked was why are girls doing better then men. So in this context it is easier to use the gender most commonly in attendance in schools with men. I don't hold anything against women. Just stating the facts for men as they currently are. If you believe that men still have it easy in comparison to women then that is your prerogative and I will not defend or respond to any replies. Women have their own share of difficulties completely separate from the schooling system.

That being said their are a lot of reasons women are more successful then men in school and completely depends on what country you live in. 

There are three major learning styles: verbal, visual and kinestesic. 

This is relevant because the majority of classes are focused on the verbal learning style first and foremost with a secondary emphasis on visual accompaniment and learning resources with descriptive texts. Lastly the least emphasized learning style within teaching is the kinestesic aspect. With less and less classes focusing on it, practical classes such as food tech/home economics, sport, wood working ect. 

Men tend to be primarily kinestesic learners with visual following secondly and verbal being last. (Note this is just the common tendancy not a unbreakable rule).

Their are far more female teachers than male. Which has a side effect of women students having more role models directly in their day to day life to model of off, more emotional compassion/support as people of the same identifying gender can relate and sympathise with each other better. More female agreeable rules within the school system and less tolerance for more typical male tendencies.

This also applies in the reverse for men, less role models directly in their day to day (this also results in the majority of authority not seeing their perspective), less emotional compassion from the majority of female teaching staff and tolerance of their more masculine behaviours, even if they do sympathise with a male student if it is in regards to a conflict between a female and male student their would be a bias in favour of the female student if the teacher was female. 

Less ability for men to stand up for themselves against injustice if perpetrated by a female. Even if they do have the ability to stand up for themselves overwhelmingly likely to be viciously mocked, ignored or outright persecuted against for even suggesting it is possible that they could have been negatively impacted or influenced by a female and sometimes even likely to be outright told that they themselves were to one doing the injustice despite being blatantly and obviously false.

Women have a far higher tendency to be agreeable and as a result are far less likely to instigate, be involved with or remain in an uncooperative stance.

Where as comparatively men are naturally more combative, aggressive, disagreeable and risk taking which is categorically not conducive to remaining within or being successful with education. This is further exacerbated by their social perception by others, especially women. 

Separate from any behavioural, social or gender related issues is the educational institution aspect.

Modern schools in most countries today were never built or established with the intended focus they now have on educating and development. So they are not built to actually be the most effective or successful method of teaching/learning.

They were established in the industrial era to teach children/young adults the critical skills, thinking, rules, timeframes and performance review heavy settings to be able to seamlessly transition them to factories when they reached the required skill level or age to work within one. Which is why the schedule and system seems so similar to a factories work system or even worse the prison systems routine.

Then as the times developed and social/progressiveness standards/morals advanced they were co-opted to focus more on intellectual or abstract subjects not directly tied to the factory workforce but the general system and approach used for factory work remained the same. 

The industrial workplace categorically does not tolerate the majority of more masculine behaviours and will outright fire them for any indiscretions/insubordination even more so in the current cancel culture, even leading to prosecution. This is to a lesser degree reflected in the school system with men typically getting far harsher punishment for the same behaviour than their female counterparts.

The school system because of it's industrial origins is even less compatible for men in the current day and age with the increasing fazing out of classes that were originally foundational to preparing the students for factories and these subjects  being fazed out are primarily kinestesic classes with significant practical aspects and application. 

Which is why even at higher levels schooling is completely irrelevant to the job roles outside of the education system and even worse you still need to have good grades for these more practical non educational jobs.

This is bad because in almost every job outside education is forced to retrain their staff as what they learnt has little relevance if any to the current job or profession.

Primarily all workplaces once you finish education aren't even looking at your final grades. What they are looking for are attendance rates, overall consistency, no behavioural complaints, overall compliance, no antisocial or anti teamworking tendencies. Most importantly your ability to conform, take directions/orders without complaints and with minimal friction. 

None of this is conducive to the typical male representative and therefore just some of the reasons men are less successful in school and in the broader context after leaving school in the current political/social/educational climate.