"Freddie Mac's departure from proper accounting practices was the result of a corporate culture that sought stable earnings growth at any cost," said Linda Thomsen, the SEC's enforcement director, in a statement.
The SEC said it expects to distribute the penalty money to investors.
Freddie Mac has taken a number of steps to bolster its accounting practices. On Thursday, Freddie's chief executive, Richard Syron, said the agreement resolves the last investigation related to its earnings restatement.
"This is another milestone enabling us to focus entirely on those things that are most important -- further advancing our housing mission, effectively serving our customers and building our business for the future," Syron said.