He says the exam, taken by 600,000 teenagers every year, should become entirely modular, with pupils being able to take a mix of vocational and academic options within each subject.
Writing in The TES, Dr Boston, chief executive of the Qualifications and Curriculum Authority, rejects calls for an end to the GCSE. Instead he sets out a vision in which teenagers from the age of 14 would build their own qualifications from a series of increasingly challenging "units". He says that his proposal would help end the academicvocational divide, which pigeonholes too many students at the age of 14.
The article is the first detailed proposal about how a revised GCSE might fit within the Government's plans for a baccalaureate system for 14 to 19-year-olds. It comes as the exam faces serious criticism from teachers who have contacted The TES website complaining that schools are bending coursework rules to improve pupils' marks.
Under Dr Boston's proposals, every GCSE would essentially become a "hybrid" qualification with academic and vocational elements. Each student would sit a series of compulsory or "general", units in subjects including English, maths, science and computing.
He envisages that the units would build on each other, with perhaps three levels of difficulty and, crucially, the ability to combine vocational and academic study.
"We need to replace pathways with stepping stones, to provide accumulating career and training opportunities that open up in front of people rather than closing off behind them," Dr Boston writes.
"The purpose would be to allow young people to navigate their own way according to interest and aptitude, by selecting combinations of units which build the qualification in a way which suits the student."
His vision is a rejection of calls by his predecessor David Hargreaves and the National Association of Head Teachers for the GCSE to be scrapped. He argues that the present GCSE fails to provide a "sound foundation" on which to build an English baccalaureate because, unlike other qualifications, it is not modular.
Dr Boston's views will be controversial. The model is similar to that planned for the new "hybrid" science GCSE, being introduced in September.
The new qualification includes a compulsory core which skips much of the theory traditionally taught at this level. A 14-year-old taking the applied route would lack the theoretical knowledge to go on to A-level.
Ministers are unlikely to offer a response to Dr Boston until former chief inspector Mike Tomlinson finishes his inquiry into 14 to 19 provision at the end of the year.
John Dunford, general secretary of the Secondary Heads Association, said:
"This is something we have been advocating for the past 12 to 15 years. AS and A-levels have a modular structure. It would be folly to have one structure of qualifications up to 16 and another after."
But David Hart, general secretary of the National Association of Head Teachers, described the plans as only a "temporary solution". Ministers should abolish the GCSE in favour of more rigorous tests to allow pupils to go on to five years of study without external exams.