There's lots of reasons why this could be the case(Hi, I work in a High School and we have had training and done studies on WHY this is the case and there's a really bright dude, a former teacher, who specifically focusses on Raising Boys Achievement and he has come to our school many times and makes such excellent points)

One potential reason is that boys are prevalently kinasthetic learners-they learn by doing which most schools can't/wont cater for. Sitting in a class, listening, answering questions does nothing for their ability to retain that knowledge. Schools which can allow for learning by doing show huge improvements in boys attainment.

There's also things you wouldn't expect, like the way boys clothes are labelled; t shirts for five year olds which suggest little boys are trouble/naughty/little monsters can have interesting effects on how they then approach academics as they age. It pushes them away from the idea learning can be cool and sets up the future anti intellectualism some boys appear to display.

Then you have funny things; Boys are not encouraged to be neat and tidy. Especially in handwriting. Since boys often get talked down to or told off for bad hand writing, hand writing they are never given the time and space to improve on. As a result they either try less hard on their class and homework, or come exam periods even if they are very bright their exams/course work is harder to read and so they're marked down on appearance/spelling by an examiner who can't or wont spend the time trying to decipher the text.

Then there are factors like race, cultural or religious background ad their feelings about their place in society. Boys, especially from specific racial or religious groups are more likely to feel disenfranchised or disillusioned with the entire 'System' and as their first encounters with 'The System' are via their education then they don't always feel compelled to press themselves and try as hard.

They're also just not expected to do as as well and because they're not expected to, they find less encouragement from adults around them and therefore, continue not to try that hard.

It's sad, incredibly sad. So many of the boys I work with are bright, intelligent young men but sit them in front of an exam paper and they lose the ability to string two sentences together.