Mr Fleming, the former chief operating officer at Merrill Lynch, will join the firm in February 2010.
He will be reporting to his former Merrill Lynch colleague James Gorman, who is set to take over as Morgan Stanley's chief executive officer next month.
Mr Fleming said: "I have long admired Morgan Stanley as a pre-eminent global franchise.
"I have enormous respect for James and the calibre of the team he is assembling."
Mr Fleming joined Merrill Lynch in 1992 as an investment banker and went on to hold a number of important executive positions at the firm.
These included chief operating officer of global investment banking and co-president of Merrill's Global Markets and Investment Banking Group.
Merrill Lynch was sold to Bank of America for $50 billion in September 2008 at the height of the financial crisis.
By Gary Cooper