Williams will continue to serve as CEO until a successor is chosen.
As CEO, I have focused the company on providing the necessary funding to support sustainable homeownership and quality affordable housing; creating the solutions needed to stabilize the market and help homeowners in distress; and building a strong new leadership team that can move the company and the industry forward,” said Williams in a statement.
“For the past three years, we have executed on this important mission, while making fundamental changes to prepare housing finance for a better future. I decided the time is right to turn over the reins to a new leader. As I told our employees today, I am extremely proud of what we have achieved together, and I am confident that they will continue to make a positive difference,” he said.
The future of Fannie Mae and Freddie Mac, the two largest guarantors of U.S. residential mortgages, remains uncertain. Charles Ed Haldeman, CEO of Freddie Mac, announced last year that he is also leaving the company. Some government officials are calling for the two agencies to be shut down.
However, Fannie and Freddie's massive portfolios would take years to unwind and they remain a critical housing stabilizer in the absence of private investment, said housing experts.
In November, officials from Fannie, Freddie and its regulator, the Federal Housing Financing Authority, testified before Congress after elected officials expressed outraged over executive compensation following the government takeover of the firm in 2008.
Fannie and Freddie have cost taxpayers more than $150 billion since going into conservatorship, after they risked becoming insolvent in the face of mortgage losses. Williams' compensation was $5.59 million in 2010, according to Forbes.
Williams became president and CEO of Fannie Mae in April 2009, replacing Herbert Allison, who served as CEO from September 2008, when the company was taken over by the government. Daniel Mudd, who oversaw the firm prior to the credit crisis in 2008, is being sued by the SEC, along with five other former executives of Fannie and Freddie.
Williams was previously the company's executive vice president and chief operating officer and had worked in its eCommerce and eBusiness divisions. He joined Fannie Mae in 1991. He previously worked at accounting firm KPMG Peat Marwick and Dupont.