Friday at the White House, Mr. Obama thanked Jones for his contributions, calling him a “steady voice” in the administration’s meetings and decision making.
The president announced that deputy national security adviser, Tom Donilon, would succeed Jones in what the president called one of the most difficult jobs in the U.S. government.
Mr. Obama said Jones had agreed to serve as national security adviser for two years when accepting the role in early 2009.
Prior to working in the Obama White House, James spent nearly 40 years in the U.S. military.
The announcement follows the resignation in recent months of several other senior Obama administration officials. Last week, the president’s chief of staff, Rahm Emanuel, left his post to run for mayor of the city of Chicago.