A Secondary Heads Association publication says that boys are four times more likely to fail than girls who are now dominating achievement at every educational level.
In 1995, girls equalled or bettered boys' results in every GCSE subject except double-award science.
Peter Downes, one of the authors and a past president of SHA, said the situation is so bad that more academic selection would lead to a gender-based apartheid.
Grammar schools would be filled with high-flying girls while their brothers languished in secondary moderns.
"We would be creating ghettos," said Mr Downes, who was formerly head of Hinchingbrooke School in Cambridgeshire.
He added: "A typical 13-year-old boy can concentrate for four or five minutes while the girl can concentrate for 15 minutes. Boys prefer active learning, while girls are happy to work on projects alone."
Can Boys do Better? is written by three headteachers, Mr Downes and an educational consultant.
It suggests that girls are predisposed by both nature and nurture to do well: "The nub of the matter seems to lie in a combination of social factors and levels of literacy.
"Not only are girls better readers than boys at the age of 11, but they are also hard-working, organised and have a greater sense of their individual progress than boys."
While accepting that there are no "quick fixes", the book outlines successful attempts by some schools to tackle the problem.
At Moulsham High School in Chelmsford, Essex, boys and girls are taught separately in the early years, and for all core subjects at key stage 4 -despite the extra cost of effectively running two schools.
Woolwich Polytechnic School in the London borough of Greenwich and Okehampton College, Devon, have had some success through setting short-term targets for boys.
Somerset has found boys respond better to firm deadlines, strict homework checks, and consistently applied sanctions. It believes boys favour silent classes and a large proportion of teacher-led work.
Can Boys Do Better? is available from MAPS (Secondary Heads Association) Ltd, 130 Regent Road, Leicester, LE1 7PG, price Pounds 7.00