The President's joint press conference with Iraqi Prime Minister Nouri al-Maliki was interrupted when a local journalist called him a "dog" in Arabic before throwing his footwear at him from 25 feet away.
Mr Bush ducked the first missile and it hit a wall behind him. As a second shoe flew through the air, secret service agents dragged the assailant from the room.
The president shrugged and joked: "I'm OK. All I can report is a size 10." Later, he said: "It's like going to a political ally and having people yell at you."
"I've seen a lot of weird things during my presidency and this may rank up there as one of the weirdest.
"On the other hand, I do remember when the president of China came to the South Lawn, and a member of the press corps started yelling. I think it was Falun Gong slogans at the Chinese president. So this happens and it's a sign of a free society."
The president played down the significance of the incident, saying: "I don't think the Iraqi press corps as a whole is terrible. And so, the guy wanted to get on TV and he did. I don't know what his beef is. But whatever it is I'm sure somebody will hear it."
Mr Bush's visit to Baghdad occurred just 37 days before he hands the war off to his successor, Barack Obama, who has pledged to end it.
"The war is not over," Mr Bush said, adding that "it is decisively on it's way to being won."
Nearly 150,000 US troops remain in Iraq. More than 4,209 members of the US military have died in the conflict since it began almost six years ago.
Polls show most Americans believe the US made a mistake in invading Iraq in 2003.
Mr Bush ordered the nation into war against Saddam Hussein's Iraq while citing intelligence claiming the Mideast nation harboured weapons of mass destruction.
The weapons were never found, the intelligence was discredited, Bush's credibility with US voters plummeted and Hussein was captured and executed.
"There is still more work to be done," Bush said after his meeting with Iraqi Prime Minister Nouri Maliki.
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