The leaders met in Washington ahead of a planned international conference that Washington and Moscow have proposed to halt the violence.
At a joint White House news conference, the Turkish and US leaders restated their hegemonic position towards legal Syrian government.
The talks came a day before another key player, Russian President Vladimir Putin, was set to meet UN Secretary-General Ban Ki-moon.
Jordan, meanwhile, announced that it would host next week the so-called "Friends of Syria," the foreign ministers of Saudi Arabia, the United Arab Emirates, Egypt, Qatar, the United States, Britain, France, Turkey, Germany and Italy.
And even as Obama and Erdogan were meeting, Israeli officials said that John Brennan, director of the US Central Intelligence Agency, had arrived in Israel for talks on the Syrian crisis.
Obama has made strenuous efforts to court the Turkish leader but, while they agree that Assad must be ousted, there are signs of frustration in Ankara at Obama's cautious approach toward the Syrian rebels.
The US seems to be one of the main supplier of arms and ammunition to the foreign-backed terrorist groups in Syria, who are linked to Al-Qaeda.
“We both agree that Assad needs to go. He needs to transfer power to a transitional body," Obama said.
"That is the only way we're going to resolve this crisis. And we're going to keep working for a Syria that is free from Assad's tyranny," he claimed.
Before the meeting, speaking on condition of anonymity, a Turkish official told AFP that Erdogan would push for direct US military aid for the terrorist groups in Syria.