Bedales, a Hampshire school founded in 1878, 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 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 shunning the 18-year-old exam.
This week, The TES Cymru learned that next year's league tables in England are likely to be without many top-performing private schools because they have abandoned conventional maths and English GCSEs.
Central to the schools' concerns is a feeling that GCSEs encourage "teaching to the test" instead of promoting independent thinking among pupils, and that acquiring many passes is pointless.
GCSE results published yesterday reveal a 98.1 per cent pass rate in Wales, the same for the UK as a whole. The proportion of Welsh exam entries meriting an A*-C grade was also up, by one percentage point, to 62.3.
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 exams. 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 two others of their choice. Traditionally, most have taken 10 or 11 GCSEs.
They will then choose up to three from 10 in-house courses including theatre arts, philosophy, and religion and ethics. All will be taken through coursework, marked by teachers and externally checked.
Staff at Bedales believe GCSEs are now a turn-off for imaginative students and that the process of achieving high grades has become anti-educational.
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 and foreign cultures. 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.