The session was not a formally planned moment of diplomacy but rather a late add-on to let the two men continue their conversation from a group dinner the night before.
"We have a very complicated and quite substantial relationship with China across the board," White House National Security Advisor Tom Donilon told reporters after the session.
"We do have economic issues, they are around the proper contribution that the Chinese make to global growth and that goes to currency and other policies," he added.
He said Obama stressed the importance of China adjusting the value of its currency, which the United States contends is deeply undervalued. He said Obama and Wen also briefly discussed territorial disputes in the South China Sea toward the end of their meeting.
But Donilon also downplayed tensions between the two powers, saying the two countries also have found vast areas of agreement. The meeting came on the last leg of Obama's nine-day Asia-Pacific trip, in which he has focused on bulking up America's presence in the region, including setting up a Marine task force in Australia, in moves largely seen as hedges against China's rise.