Obama sent the letter last month to Ayatollah Ali Khamenei and described what he called a "shared fight" against the Sunni militant Islamic State group, the Wall Street Journal said, citing "people briefed on the correspondence."
Iran, a Shiite Muslim state, and the United States have not had diplomatic ties since the 1979 storming of the American embassy in Tehran and the 444-day hostage crisis.
But there has been a growing recognition that Iran -- still dubbed by Washington a state sponsor of terrorism -- could play a role in helping to restore stability in countries such as Iraq and Syria.
Iran and the United States are currently negotiating a complex deal to rein in Iranian nuclear ambitions in exchange for an easing of crippling international sanctions against the Islamic republic.
Also Read
Earnest repeated that on the sidelines of those talks, being led by a group of powers known as the P5+1, Iran and the US had discussed the threat of the militants.
But he reiterated the US stand that "the United States will not cooperate militarily with Iran in that effort, we won't share intelligence with them."
The Journal said it was believed to be the fourth letter from Obama to Khamenei since the American leader took office in 2009. US officials told the paper that the Iranian leader has never responded personally to the overtures.
Many of Washington's regional allies, including Israel as well as Saudi Arabia, have been wary of the US administration bid to engage Iran diplomatically, and the Journal's sources said the White House did not tell those countries in advance of Obama's letter.
They will meet in Muscat, which hosted secret Iran-US talks in 2012, widely credited for bringing Tehran back to the nuclear negotiations.