In a note to department staff, LaHood said he would remain at the helm until a replacement is confirmed to ensure "a smooth transition for the department and all the important work we still have to do."
The former seven-term congressman from Peoria, Ill., has led the department since 2009 and was not expected to stay on through a second term. Among those who have been prominently mentioned as a possible successor is Los Angeles Mayor Antonio Villaraigosa, whose mayoral term ends June 30 and who played a key role in writing a provision of last year's federal transportation bill that is designed to speed up projects throughout the country, including in Los Angeles.
The White House did not immediately comment on possible replacements.
In a statement Tuesday, Obama, who worked with LaHood in Congress, praised the secretary's bipartisanship.
"Years ago, we were drawn together by a shared belief that those of us in public service owe an allegiance not to party or faction, but to the people we were elected to represent. And Ray has never wavered in that belief," the president said.
LaHood was brought into the Cabinet as a symbol of a new bipartisan era Obama planned in his first term. But the Republican's views quickly seemed out of step with his party and did little to bolster the president's standing with the opposition.
In his note to staffers, LaHood listed his top accomplishments during his tenure, including a program to curb texting while driving, fighting pilot fatigue and the more than $50 billion spent on transportation projects as part of the president's stimulus package, a program opposed by most in the GOP.
"We helped jump start the economy and put our fellow Americans back to work," LaHood wrote. "Our achievements are significant."
Obama has nominated another Republican to his second term Cabinet. Former Nebraska Sen. Chuck Hagel, if approved by the Senate, will become secretary of Defense.
Staff writer Richard Simon contributed to this report