The talks, in the secure Situation Room of the White House, went ahead amid a rumbling US disagreement with Islamabad on the fight against militants in the volatile Afghan-Pakistan border region.
At Obama's side in the talks were Defense Secretary Robert Gates, UN ambassador Susan Rice, National Security Advisor Tom Donilon and James Clapper, his director of national intelligence.
Vice President Joe Biden, top Afghan war General David Petraeus and the US ambassadors to Pakistan and Afghanistan joined the session via secure video-link, the White House said.
The White House said that officials briefed Obama on the security situation in Afghanistan, efforts to build national Afghan forces and efforts to ensure cooperation with Pakistan in the fight against Al-Qaeda.
On Saturday, Pakistan's army chief General Ashfaq Kayani said that the "backbone" of militants in Pakistan had been broken, despite US criticisms of his country's strategy against Taliban and Al-Qaeda-linked rebels.
The White House criticized Pakistan's efforts to defeat the Taliban in its border regions, in a report immediately rejected by Islamabad earlier in April.
Obama is also beginning to reach the point when he must consider recommendations by the military for the promised partial withdrawal of troops from Afghanistan, which he has demanded from July this year.
However, his press spokesman Jay Carney said that Monday's session was not a "decisional" meeting, but was rather a regular review of US policy.
There are signs that any drawdown of troops from the decade-long fight against the Taliban will be mainly symbolic as Washington and its allies increasingly focus on the security "transition" from foreign to Afghan control.
The administration has gradually de-emphasized the timeframe, instead saying that most US forces would leave in 2014 -- the date set by last year's NATO summit for putting Afghans in charge of their own country's security.