The Pentagon’s second-highest-ranking civilian said Thursday that he plans to leave his post later this summer or early fall after new Defense Secretary Leon Panetta has had time to choose a successor.

Deputy Defense Secretary William J. Lynn III is resigning at a time when senior officials in the department are weighing how to best cut more than $400 billion from the defense budget over the next 12 years. His departure means that the top three officials in the Pentagon will all be relative newcomers to their jobs. Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff, will leave his post on Oct. 1 at the end of his four-year term.

Lynn’s resignation, which has been rumored for several weeks, was spurred by his desire to spend more time with his family, said defense officials. “The secretary asked me to stay to ensure a smooth transition” to a new deputy, “and we think that’s probably early fall,” Lynn told the Associated Press. “I think they’ll try to move pretty quickly.”

Although Lynn has a wealth of experience with defense budget issues, one outside observer said he seemed to struggle to find his place in the Pentagon under Robert M. Gates, Panetta’s predecessor.

“Gates tended to turn to his chief of staff, Robert Rangel, to lead the most important initiatives, like finding efficiencies in the defense budget,” said Loren B. Thompson, the chief operating officer of the Lexington Institute, a Washington-based think tank. “Lynn got cut out of a lot of the action.”

A Pentagon spokesman disputed Thompson’s characterization and said that Lynn was deeply involved in Gates’ efficiency effort, along with a host of other key initiatives in the department. “He led several major cross-cutting initiatives, including the development of the department’s first-ever cyber-security strategy, a new space policy, an improved wounded warrior transition effort with the Department of Veterans Affairs,” said Bryan Whitman, the spokesman. “And he did it all while overseeing the day-to-day operations of the department.”

Lynn, 57, came to the Pentagon in February 2009 and has focused much of his time on developing the military’s strategy for securing its computer networks. The strategy overseen by Lynn focused on what he called “active defense,” blocking malicious software before it arrived “at the door” of military networks.

The new cyber-security strategy is to be announced next week.

The front-runners to replace Lynn include Navy Secretary Ray Mabus and Ashton B. Carter, the undersecretary of defense for acquisition, technology and logistics. Both played an important role in repairing the Navy’s troubled ship-building program and the massive F-35 fighter-jet program.

Michele Flournoy, the undersecretary of defense for policy, is also rumored to be among those considered for the post. Although Flournoy is a White House favorite, she hasn’t been deeply involved in budget and military hardware issues that normally fall to the deputy. Rather, she has been more focused on U.S. military policy in Afghanistan, Iraq and South Asia.