The meeting will take place at the level of heads of state or government and coincide with the annual United Nations General Assembly, according to US envoy Samantha Power.
It will be the second time that Obama chairs a meeting of the top world body. In 2009, he presided over a meeting on nuclear non-proliferation.
The United States currently holds the rotating presidency of the 15-member council.
"We are seeing a surge in terrorists travelling from around the globe specifically to fight in foreign conflicts," Power said.
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A senior US intelligence official estimated yesterday that more than 12,000 foreign fighters had travelled to Syria to battle President Bashar al-Assad's regime, including more than 1,000 Europeans and more than 100 Americans.
Many had joined the ranks of the so-called Islamic State, blamed for the two recent beheadings of American journalists James Foley and Steven Sotloff, according to Matthew Olsen, director of the National Counter-terrorism Center, a US government organisation.
Power said Washington would be seeking consensus on the severity of the threat of such fighters and the need for collective action, adding that discussions were under way on a resolution on the matter.
"We are very confident that this resolution will secure consensus," she said. "This resolution will pave the way for national governments to do more.