Bank of New York Mellon Corp
The company, one of the world's largest custody banks, said it named board member Gerald Hassell as chairman and CEO, effective immediately.
Kelly's resignation was by mutual agreement with the board, BNY Mellon said in a statement.
Kelly, who served as CEO of Mellon Financial Corp prior to the merger of Bank of New York and Mellon Financial, took home $19.4 million as compensation in 2010.
Trust banks have avoided many of the credit issues that have weighed on larger traditional banks, but shares of BNY Mellon and its main rival State Street Corp
The company, which also competes with Northern Trust
Earlier this month, BNY Mellon said it would cut about 1,500 jobs, or 3 percent of its workforce, to cope with rising costs.
Shares of the company were down 3 percent in trading after the bell. They closed at $20.67 on Wednesday on the New York Stock Exchange.
(Reporting by Brenton Cordeiro; Editing by Anil D'Silva)