Boys thrived in the rules-based school environment of days gone by where discipline was firm and consistent and every action had a clearly-defined consequence.
The school system rewards girls for being girls and treats boys like miscreants or defective girls. This creates an environment where boys miss more school for disciplinary issues and resent the way they are treated at school, both of which negatively impact male academic performance.
Typically female interests, like socializing with peers and being creative, are rewarded in the school environment. They are encouraged to collaborate and express themselves through words, art and music. Typical male interests, however, like roughhousing, running around and expressing themselves through movement and hyperactivity, are punished in schools.  Additionally, more young girls like to read, while many young boys prefer to play sports. This means while girls are building verbal proficiency and comprehension skills, both useful in academia, boys are developing hand-eye coordination skills, teamwork, and athleticism, none of which are useful in the classrooms or exam halls. Finally, the subject matter taught in schools now favours female student participation. In the past, students studied Macbeth, Julius Caesar and Coriolanus, plays with masculine protagonists engaging in battles and facing down adversity. Now, the curriculum favours plays like Romeo and Juliet and literature from the Bronte sisters, Jane Austin and George Eliot, which appeal more to female audiences. This war on boys’ interests only leads to more male students resenting the classroom environment, which leads to more boys misbehaving in class and then results in more missed class time due to disciplinary proceedings. This vicious cycle leaves boys underperforming at all levels and failing to thrive in the classroom. This systemic issue is reflected in studies of the attitudes of male students towards their schools and teachers. Even boys that perform well academically often hold more negative views of their school, their teachers and their female peers, than female students do.
This has always been the case. In the past, boys were disciplined for speaking out of turn and not focusing. They would have their knuckles rapped with the cane for roughhousing and messing around with other children when they should have been sitting quietly, yet girls have not always outperformed boys. Girls have only recently begun outperforming boys in the school system. If the war on boys’ interests leads to boys underperforming in school, why have they not always underperformed in academic environments? Also, the assumption that boys prefer sports while girls prefer to read is flawed. Female participation in sports during the early school years is almost the same as boys. Also, the number of girls participating in sports is increasing, but so is the academic gap between girls and boys. Therefore, the fact that boys play sports cannot be a driver of academic underperformance. By contrast, there is evidence to suggest that students that play sports outside of school perform better academically. They have higher attendance rates and lower school and college drop out rates. 
[P1] Schools reward female interests and discourage male interests. [P2] This leads to disciplinary issues and disengagement from academia. [P3] This results in lower academic performance.
[Rejecting P3] Schools have always disciplined students for not focusing and asked them to sit still. But girls have not always outperformed boys.