This is despite the failure of local education authorities to provide equal opportunities support and despite a persistent "culture of male management" in schools, says the report, written by academics at Cambridge and South Bank Universities.
Separate research from the University of East London this week confirmed that schools are still overwhelmingly run by men though the majority of teachers are women.
The EOC report is the latest in a series of recent studies demonstrating the remarkable improvement in girls' performance at GCSE since the mid-1980s.
The apparent failure of white working-class boys to respond is an increasing cause of concern and was recently described by Christopher Woodhead, the chief inspector, as "one of the most disturbing problems we face within the whole education system".
The report says that over the past 10 years, girls have been entering the full spread of GCSE subjects (with the exception of chemistry and economics) in ever greater numbers.
In terms of achievement, it says that female results have improved "markedly", while boys have failed to match them.
In 1994 single-sex schools for girls produced higher overall grades than single-sex boys' schools. Girls also produced higher performances in six out of seven types of mixed school, both selective and non-selective.
While welcoming the girls' performance, the commission expressed concern that boys continue to dominate in vocational courses. It criticised continuing high levels of sex stereotyping in vocational choices with girls choosing hairdressing and beauty and the caring services while boys plump for engineering and construction.
The report found that girls have produced a marked improvement in A-level results, but that the overall advantage still lies with boys. Young men have increased their entry advantage in chemistry and mathematics as well as improving their take-up of traditionally female subjects like English and modern languages.
"The research revealed a mixed picture of beneficial procedures and policies, " says the report, "with some thoughtful and knowledgeable practice from committed individuals and groups, but overall no infrastructure for the delivery of equal opportunities on a wider and more systematic basis."
Local authorities did not appear able to match their promises about delivering support for equal opportunities.