McCain's visit was kept secret, and he was believed to have been in the country for several hours before reporters were able to confirm his presence. It was unclear who he met on arrival.
Ahead of the trip, McCain reportedly insisted it was a fact-finding venture, not a campaign photo opportunity.
He is scheduled to meet General David Petraeus, the top US commander in Iraq, during the day.
McCain's weeklong trip also includes stops in Israel, Britain and France - all countries where he has made many visits in the past.
Ahead of the trip, McCain expressed worries that anti-government fighters might try to influence the November general election with increased attacks in Iraq.
"Yes, I worry about it," he said on Friday in Springfield, Pennsylvania. "And I know they pay attention, because of the intercepts we have of their communications."
McCain told reporters later that al-Qaeda remains smart and adaptable despite an increase of US troops in Iraq.
A defiant supporter of the 2003 invasion and President George Bush's troop increase last year, McCain has touted last year's drop in sectarian violence as a turning point in the five-year war.