The stake will be sold to BNY, giving it complete control over the Dublin-based firm, called AIB/BNY Securities Services.
The company provides administrative services to funds based in Ireland, with an estimated $210 billion in assets currently being handled.
Commenting on the agreement, the details of which have not been released, Mon O'Driscoll, head of investment banking at AIB Capital Markets, said that despite the success of the venture it was time for BNY to take control.
"The agreement reached today is a natural and correct strategic decision for both AIB and BNY," he said.
AIB/BNY Securities Services was established in 1995, with the net assets of the joint venture currently at $28.8 million.
The deal will see all 600 AIB employees move over to BNY.