Rooney quit Baltimore in July 2001 after the company's shares fell 95 percent in seven months, making them the worst-performing stock on the FT-SE Techmark 100 index so far that year.
Rooney replaces Brendan Menton, who resigned after a damning report into the build-up to the 2002 World Cup tournament in South Korea and Japan.
The problems in the preparations to the tournament also saw Reupblic of Ireland captain Roy Keane return home early after stating that FAI executives didn't pay enough attention to players.
Rooney's wealth has tumbled as shares in Baltimore fell although he was named as one of Ireland's 100 richest people in 1998, 1999 and 2000 by the Sunday Times newspaper.
Rooney will take up the job in June, having previously managed Ireland's women's soccer team.
Fran Rooney, formerly chief of Baltimore Technologies, is to take over as chief executive officer of the Football Association of Ireland.
