Mr. Leiter, 42, one of the few senior national security officials from the Bush administration that President Obama kept on, will leave on July 8, roughly when the White House is expected to release an updated counterterrorism strategy that Mr. Leiter contributed to, administration officials said.  

Friends and colleagues said Mr. Leiter’s departure was expected, as his tenure coincided with one of the most demanding periods after the Sept. 11 attacks. Even as Al Qaeda’s leadership in Pakistan came under increasing pressure, culminating in the death of Osama bin Laden on May 2, Qaeda affiliates blossomed in Yemen and North Africa, and American officials warned of a threat from homegrown terrorists here.

In a telephone interview on Thursday, Mr. Leiter, who is newly remarried, said he was stepping down for personal reasons and to allow his successor to “bring fresh eyes to the problems we face.” He has not yet decided on his next job, he said.

As director of the National Counterterrorism Center, which was created in 2004, Mr. Leiter oversees 1,000 specialists from more than a dozen federal agencies who form the central clearinghouse and analytical hub for intelligence on terrorist threats.

Andy Liepman, Mr. Leiter’s deputy, will serve as acting director until Mr. Obama appoints a successor, James R. Clapper Jr., the director of national intelligence, said in a statement.