Teachers not the system
Teachers often let behaviour influence their grading patterns. This is what leads to male underperformance.
Boys develop non-cognitive skills slower than girls. It is not the school system that lets boys down, but their biological development.
Boys develop non-cognitive skills at a much slower rate than girls. This means that there will always be a gap between female and male learners, particularly in primary and elementary level education.
Boys develop skills like attentiveness, persistence, and the ability to sit still for long periods of time much later than girls. This means that girls will always outperform boys in school, particularly in the younger years. The lead that girls build up in the early, formative years is then gradually eroded. In a study looking at several hundred Kindergarten students, researchers from the University of Virginia examined young boys’ and girls’ abilities to self-regulate. Self-regulation is necessary for the development of disciplined behaviours like raising your hand in class, waiting your turn, following instructions and sitting still. They found that by kindergarten age (five and six) boys were already one year behind girls in the development of self-regulation skills.  Girls then carry this advantage throughout their school careers. In a study examining similar skills in middle school students, researchers found that female students are better at reading and following test instructions, completing their homework assignments, and sticking to long assignments even after initial frustrations.  Boys have still not closed the gap by the time they reach college. Researchers have found that female university students are more likely to take accurate notes in lectures and are better at remembering lecture content. The problem does not lie in the education system. It is not inherently biased against boys. Boys are just slower to mature than girls. This is a biological difference that cannot be fixed by adjusting the school system.
The research does not necessarily indicate that boys are slower to mature. It is just as reasonable to conclude from the experiences mentioned that the school system favours girls. If boys are more likely to miss important test instructions, this may not mean that their brain development is slower. It could just as easily mean that written instructions appeal to female skillsets and that audio instructions or visual instructions would result in fewer boys making examination mistakes. Similarly, the lecture model at university, where students sit still, pay attention and don’t speak, might not be the best way for male students to receive this information. As a result, female students take better notes. If the school system did not favour students with strong reading proficiency, organisational abilities, and self-regulation skills, then boys and girls might be on a more equal footing. Maybe boys are slower to mature. But it is the responsibility of the school system to take this into consideration and take steps to stop boys falling behind academically.
[P1] Boys are biologically slower to mature than girls. [P2] This is the result of biology, not systemic bias within the school system. [P3] Therefore, the male-female academic gap is not systemic, but biological.
[Rejecting P1] They are not slower to mature, they just mature faster in different areas. [Rejecting P2] The system could take steps to ensure that both female and male maturity is taken into consideration when devising curricula and examination. [Rejecting P3] The likeliest scenario is that the performance gap is the result of both schools failing to accommodate male cognitive development and biological development rates.