Bedales, a Hampshire school founded in 1893, where boarding fees are Pounds 25,000 a year, is introducing its own courses to replace all but the core GCSEs which it says are required by universities.
Brighton college, in Sussex, is barring its pupils from taking more than nine GCSEs, even though it admits this could damage its league-table ranking.
They are joining scores of private schools which are shunning the exam.
This week, The TES learned that next year's league tables are likely to be without many top-performing private schools because they have abandoned conventional maths and English GCSEs.
Annual results released yesterday showed the proportion of entries awarded passes at C or better rose to a record 62.4 per cent, with nearly one in five entries awarded an A or A*.
The schools feel that GCSEs encourage "teaching to the test" instead of promoting independent thinking. James Williams, a Sussex university lecturer in education and housemaster on Channel Four's That'll Teach 'Em, said this week that the exams were no longer a test of understanding.
He said: "Take science. Pupils can achieve the highest grades without having to write more than an A4 side in each exam. How does that test understanding?"
From next month, students at Bedales will take GCSEs in English, maths, a language and science, plus up to only two others of their choice.
Traditionally, most have taken 10 or 11 GCSEs.
They will then choose up to three from 10 courses which Bedales have developed in-house. All will be taken through coursework, marked by teachers and externally checked.
Staff believe GCSEs are now a turn-off and that the process of achieving high grades has become anti-educational. Martin Horrox, a Bedales spokesman, said: "There's a tendency to say 'do this and do this' and you've got an A grade, rather than saying the syllabus should be the minimum starting point for a process of learning.
"We do not see that as an educational process. We see that as an exercise in passing exams."
Brighton college is introducing the cap after consulting admissions tutors at Oxbridge and other universities, who say they are only interested in up to eight GCSEs.
Richard Cairns, head of the boarding and day school, which charges up to Pounds 20,500 a year, said pupils would spend additional time studying non-curricular subjects, such as current affairs. Some of England's most famous private schools, including Winchester, Harrow and Manchester Grammar are dropping GCSEs in several subjects in favour of international GCSEs.
These are not accredited for league tables, so many of these schools will be bottom of the rankings next year. For the first time, these will be based on the proportion of pupils achieving five or more passes, including English and maths.