Pupils will be unable to sit GCSEs in law, performing arts and business with economics when awarding bodies in England pull out of the north.
The AQA and OCR boards both said they would not be offering reformed GCSEs in Northern Ireland.
This came after education minister John O'Dowd retained familiar A*-G grades rather than follow England in adopting a numerical system from 2017.
Most pupils take exams offered by the north's exams board, the CCEA. However, many take papers set by boards from England too. The AQA and OCR are the two most popular English boards - there were about 40,000 entries by Year 12 pupils in 2014.
Their withdrawal from the north means numerous subjects, not offered by CCEA, will no longer be available.
Mr O'Dowd provided a list of these subjects in response to an assembly question from education committee chairman Peter Weir of the DUP.
From 2017, additional science, business and economics, expressive arts, humanities and performing arts will no longer be offered by AQA.
OCR will stop offering computing, methods in mathematics and environmental science.
Both boards will not offer law.
The AQA said it realised its decision would cause disappointment.
"It was a difficult decision to make: we'd like all our qualifications to be available to everybody. But we had to consider the practicalities of running significantly different versions of the same qualification - including the extra administration needed, and the challenge of trying to set the same standard across different countries," a spokesman said.
OCR said it reached its "difficult decision" due to "operational and financial reasons".
"We are not able to offer qualifications specific to Wales or Northern Ireland, alongside a large portfolio of different, reformed qualifications that we have developed for England," the board said.
