Michael J. Williams says he will continue as CEO and as a director until a successor is found.
"I decided the time is right to turn over the reins to a new leader," Williams said in a statement.
The government rescued Fannie Mae and Freddie Mac after the two mortgage firms suffered huge losses on risky loans that threatened to topple them.
Fannie and Freddie buy loans from lenders, package them into bonds with a guarantee against default and sell those bonds to investors. Together, the companies own or guarantee about half of all U.S. home mortgages.