Flournoy, Undersecretary of Defense for policy, "this day has announced his intention to step down and return to private life," Defense Minister Leon Panetta said in a statement.
Flournoy, who turns 51 this week, "it is clear that his decision to leave motivated by personal and family considerations," the statement said.
Flournoy and her husband, who had worked as Deputy Secretary of Veterans Affairs, has held the job in the Government due to prosecute President Barack Obama took office in February 2009 and ready to restore the balance in their lives with more time devoted to their three children, Douglas Wilson spokesman told AFP.
Flournoy has agreed to stay on through "early next year" to allow time to find a replacement for number three civilian post in the Pentagon, according to Panetta.