This was an expected move, reports CBS News producer Robert Hendin. McConnell will remain a member of the White House's Intelligence Advisory Board.
President Obama's nominee to fill the post, Adm. Dennis Blair, had his Senate hearing last week, but his expected Senate confirmation has not yet taken place.
In the meantime, Lt. Gen. Ronald L. Burgess, Jr. will temporarily serve as acting national intelligence director, reports the Associated Press. Burgess has been confirmed to become the next director of the Defense Intelligence Agency.
The AP also reports that McConnell will rejoin Booz Allen Hamilton as senior vice president, where he worked before taking the intelligence job in 2006.
In his letter to employees, obtained by CBS News, McConnell expressed his "heartfelt gratitude and deep appreciation." He also listed the accomplishments of the intelligence community during his tenure.
"Your hard work and dedication to the mission are what will make stronger integration and collaboration possible as you move forward making the [intelligence community] even more effective," he wrote. "Having worked with you side by side, and knowing your professionalism and respect for our laws and values, I am fully confident that improvements in our mission performance will continue."