Obama wrote the letter to Khamenei last month, the Wall Street Journal said. "Mr Obama stressed to Mr Khamenei that any cooperation on Islamic State was largely contingent on Iran reaching a comprehensive agreement with global powers on the future of Tehrans nuclear programme by a November 24 diplomatic deadline, the same people say," said the daily, which based its report on anonymous sources.
This is the fourth letter that Obama has written to the top Iranian leader since coming to power in 2009.
"The correspondence underscores that Mr Obama views Iran as importantwhether in a potentially constructive or negative roleto his emerging military and diplomatic campaign to push Islamic State from the territories it has gained over the past six months," The Wall Street Journal said.
Two top American Senators John McCain and Lindsey Graham expressed their outrage over the letter.
"It is outrageous that, while the cries of moderate Syrian forces for greater US assistance fall on deaf ears in the White House, President Obama is apparently urging Ayatollah Khamenei to join the fight against ISIS," McCain and Graham said in a statement.
"This is the same Iranian regime that has been complicit in the rise of ISIS by pushing a violent sectarian agenda throughout the Middle East," they said.
The White House neither confirmed nor denied the existence of the letter arguing that it would not comment on the private communications between two world leaders.
"I'm not in a position to discuss private correspondence between the President and any world leader. I can tell you that the policy that the President and his administration have articulated about Iran remains unchanged," the White House Press Secretary, Josh Earnest, told reporters at his daily news conference.
"The United States is engaged in conversations with Iran in the context of the P5-plus-1 talks to resolve the international community's concerns about Irans nuclear program, and we have also discussed on the sidelines of those talks on at least a couple of occasions the ongoing campaign that is being conducted against ISIL by the United States and now more than 60 members who are part of this broader coalition," he said.
Earnest said the US will not cooperate militarily with Iran in that effort.