Washington insiders say he will quit within six to eight months in frustration at their unwillingness to "bang heads together" to get policy pushed through.
Mr Emanuel, 50, enjoys a good working relationship with Mr Obama but they are understood to have reached an understanding that differences over style mean he will serve only half the full four-year term.
Friends say he is also worried about burnout and losing touch with his young family due to the pressure of one of most high profile jobs in US politics.
"I would bet he will go after the midterms," said a leading Democratic consultant in Washington. "Nobody thinks it's working but they can't get rid of him – that would look awful. He needs the right sort of job to go to but the consensus is he'll go."
An official from the Bill Clinton era said that "no one will be surprised" if Mr Emanuel left after the midterm elections in November, when the Democratic party will battle to save its majorities in the house of representatives and the senate.
It is well known in Washington that arguments have developed between pragmatic Mr Emanuel, a veteran in Congress where he was known for driving through compromises, and the idealistic inner circle who followed Mr Obama to the White House.
His abrasive style has rubbed some people the wrong way, while there has been frustration among Mr Obama's closest advisers that he failed to deliver a smooth ride for the president's legislative programme that his background promised.
"It might not be his fault, but the perception is there," said the consultant, who asked not to be named. "Every vote has been tough, from health care to energy to financial reform.
"Democrats have not stood behind the president in the way Republicans did for George W Bush, and that was meant to be Rahm's job."
There were sharp differences over health care reform, with Mr Emanuel arguing that public hostility about cost should have forced them into producing a scaled down package. Mr Obama and advisers including David Axelrod, the chief strategist, and Valerie Jarrett, a businesswoman and mentor from Chicago, decided to push through with grander legislation anyway.
Mr Emanuel has reportedly told friends that his role as White House chief of staff was "only an eighteen month job" because of its intensity.
Regarded as the most demanding after president, it involves controlling the president's agenda, enforcing White House message discipline as well as liaising with Congress.
His departure would regarded as another sign of how Mr Obama's presidency has been far more troubled than expected.
Mr Emanuel has privately expressed a readiness to run for mayor of Chicago, which is also his home town though he was never part of the Obama set and did not endorse the then senator in the Democratic primary in 2008.
That would however depend on Mayor Richard Daley stepping down when he is up for re-election in 2011.
The chief obstacle to taking the White House job originally was doubts about moving his three children from Chicago. According to another former Clinton official, he has let friends know that he is "very sensitive to the idea that he is not a good father for having done this".
One of Washington's more colourful characters, Mr Emanuel is the son of Jewish immigrants and was an accomplished ballet dancer at school. He served as a civilian volunteer with the Israeli Defence Force in the 1991 Gulf War.
The White House did not respond to a request for comment.