(Francois Mori — Associated Press)

William Lynn has served as deputy secretary of defense since 2009, running much of the Pentagon’s day-to-day operations. He previously served as a senior adviser to five secretaries of defense.

In an interview, he told the Associated Press that he was leaving for “personal, family reasons,” and wanted to spend more time with his children.

“I thought this was a logical point for me to depart the Pentagon,” said Lynn, a former lobbyist for Raytheon.

The Defense Department is in the midst of a major shakeup. Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, is retiring in October, and Gen. David Petraeus is expected to take the helm at the CIA in September. Adm. Gary Roughead, the chief of naval operations, is scheduled to retire in September.

Lynn’s resignation had been rumored for some time. He has told Defense Secretary Leon Panetta that he will stay in his post until his successor in in place this fall.