In a regulatory filing Tuesday, Fannie Mae did not say why Chief Financial Officer David Johnson is leaving. It said that until a successor is named, Deputy CFO David Hisey will take on Johnson's responsibilities.
A message seeking further comment was left with a Fannie Mae spokeswoman.
Washington-based Fannie Mae and sibling Freddie Mac own or guarantee about half of all U.S. mortgages. They buy home loans from lenders, package them into bonds with a guarantee against default and sell them to investors.
The two companies nearly went under in September 2008. The government rescued them and estimates that will cost taxpayers up to $259 billion.