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Mayopoulos' promotion from general counsel takes effect on June 18, the company said in a statement. He will succeed Michael Williams, who in January announced his plans to step down.
"I am honored with this extraordinary opportunity to lead Fannie Mae during this critical period," Mayopoulos said in the statement. "We have a responsibility to return value to taxpayers and to contribute our expertise and experience to building a more effective and stable housing finance system for the future."
Fannie Mae and its smaller rival, Freddie Mac
Fannie Mae last month posted its first profitable quarter since being taken over by the government.
Mayopoulos, 53, joined the company as its general counsel in the spring of 2009. He previously worked as a general counsel for Bank of America
The promotion means a pay cut for the new company head. In March, the regulator for Fannie Mae and Freddie Mac unveiled a compensation plan that targets chief executive salaries at around $500,000 per year, down from base pay of $900,000.
Previously, Fannie and Freddie CEOs could earn as much as $6 million with deferred pay and bonuses.