The two largest English GCSE exam boards have said they will no longer offer GCSE courses in Northern Ireland.
The change will come into effect for pupils beginning GCSE courses in September 2016.
About a quarter of courses taken by pupils in Northern Ireland are taken through the AQA and OCR exam boards.
In England, pupils beginning GCSEs in September will move to a numerical results system, where nine is the highest grade and one the lowest.
However, in November 2015, Education Minister John O'Dowd decided to maintain A*-G grades in Northern Ireland.
AQA and OCR have said they will not operate two separate grading systems.
As a result, both have decided not to offer any more GCSEs in Northern Ireland.
Mr O'Dowd said: "It is very disappointing that some organisations are choosing to put commercial interests ahead of the needs of our young people.
"However, this response by some awarding organisations is not unforeseen."
Dermot Mullan, the principal of Our Lady and St Patrick's College in Belfast, said the move would create many problems for schools.
"We have almost a quarter of our GCSEs through those exam boards at present," he said.
"We are going to have to find an alternative examination board, and that means for staff that new specifications will have to be resourced and prepared for.
"We have built up a long relationship with AQA and OCR over 20 years.
"Being insular and looking in on ourselves with examination boards isn't a good thing for staff, schools, children and Northern Ireland."
In 2015, 25.1% of GCSEs studied by Northern Irish pupils were through the AQA, OCR, Edexcel or WJEC exam boards - which equates to about 43,000 GCSE entries.
The vast majority of those exams were taken through AQA and OCR.
About 128,000 GCSEs - 74.9% - were taken through the NI Council for Curriculum, Examinations and Assessment (CCEA).
As a result, schools will now have to offer almost all their GCSE courses through CCEA, although some may use WJEC, which is also retaining the A*-G grading.
In a statement to the BBC, Pearson, which owns the Edexcel exams, said that they had "not made a decision yet" on whether to offer a separate alphabetical grade system for Northern Ireland.
Pupils who are currently studying GCSEs under AQA and OCR will not be affected as transitional arrangements will be put in place for them.
The two boards will continue to offer A-Level courses in Northern Ireland.
GCSEs (General Certificates of Secondary Education) are the main qualifications taken by 14- to 16-year-olds in schools and colleges in England, Wales and Northern Ireland. But you can take them to gain a qualification in a subject you’re interested in at any age.
GCSEs are usually studied full time, taking two years to complete, however adult learners can take evening classes or teach themselves. Short course GCSEs are also available in selected subjects. There are no formal entry requirements and no age limits for GCSEs.
GCSE courses mainly involve studying the theory of a subject combined with some investigative work. Each qualification is at Level 1 or 2 on the National Qualifications Framework, depending on the grade you achieve. Highly valued by schools, colleges and employers GCSEs are the first step towards a range of careers or further study. GCSEs have been used as a benchmark to judge student ability for more than 25 years.
GCSEs are subject-specific qualifications. Our Edexcel GCSEs are available in over 40 subjects ranging from Art and Design to Urdu. You can see what GCSE subjects we offer and what each course covers by reading the course details, which you can download from each GCSE subject page. Find out more about qualification frameworks on the gov.uk website.
To find out more about our GCSE subjects and the support available, select a subject from the GCSE homepage:
View our Edexcels GCSEs