The literacy and numeracy signature programme created the equivalent of 270 extra full-time teaching posts and cost £16m.
It helped 19,000 pupils struggling with English and Maths.
This was in around 300 selected primary and post-primary schools.
Education Minister John O'Dowd said it was "disappointing" the scheme could not continue.
It began at the start of the 2013 school year, with £14m funding from OFMDFM topped up with £2m from the Department of Education.
Schools where some pupils were struggling to reach basic standards in English and Maths were provided with an extra member of staff.
Only newly-qualified teachers could apply for the new two-year posts.
Holy Cross Boys Primary School in north Belfast was among the schools to benefit from the scheme, gaining one new teacher.
Vice-Principal Chris Donnelly said that this had made a big difference.
"In this school two years ago, we had 68% of our children at level four in Maths and English at the end of Primary Seven," he said.
"After one year of signature, we went up to 74% and this year we are recording 80%, which is a significant leap."
Level Four is the Northern Ireland average for Maths and English at the end of Primary Seven.
Gerard Wallace is the signature teacher employed at Holy Cross since 2013, and he now faces losing his job at the end of the school year.
"I'm extremely worried about getting a job afterwards, not because I haven't got the skills, simply because the jobs aren't there for newly-qualified teachers and those as fresh as I am," he said.
A recent review found that 69% of post-primary schools which had received help under the scheme showed an improvement in the numbers of pupils achieving five or more GCSEs at grades A* - C.
In supported primary schools over three-quarters of pupils on average reached level four or above in English and Maths.
Principals called for the scheme to be extended, but the Education Minister John O'Dowd said he did not have the money as his department faced "one of the most challenging financial environments in decades".
He said, however, that the programme was leaving "an important legacy, clearly demonstrating improved attainment, and enabling our most deprived children to remain in education".
A scheme which gave extra staff to schools and two years' work to newly-qualified teachers is not being renewed due to a lack of ongoing funding.