The resolution requires all countries to adopt laws that would make it a serious crime for their nationals to join jihadist groups such as Islamic State and Al-Nusra Front.
Obama described the resolution as "historic" at the special session of the Council, only the sixth time in UN history that the council was convening at the level of heads of state.
The US president opened the session by voicing solidarity with France after one of its citizens was kidnapped and beheaded by jihadists in Algeria linked to the Islamic State group.
The resolution states that "nations must prevent the movement of terrorist or terrorist groups through their territory and ensure that domestic laws allow for prosecution of those who attempt to do so," he said.
About 15,000 foreign fighters from 80 countries have joined the ranks of jihadists in Syria, according to US intelligence estimates.
The call for action to stem the flow of foreign fighters is fueled by fears that new terror networks will emerge from the Syria-Iraq front, much in the same way that the September 11, 2001 attacks were linked to the Taliban and Al-Qaeda in Afghanistan.
Obama appealed to countries to join the US-led coalition against the Islamic State during an address a few hours earlier to the UN General Assembly.
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