The area has been a stronghold for the Taliban, who fled Afghanistan after a US-led invasion removed them from power in 2001.
Kabul and Washington have said in recent weeks that Pakistan is not doing enough to prevent fighters crossing into Afghanistan, where they often launch attacks on US and Nato forces.
The two presidents and Abdullah Gul, their Turkish counterpart, said after the meeting that their governments would "strengthen trilateral co-operation to confront the scourge of terrorism in all its forms."
The leaders agreed that their militaries and intelligence agencies should work together on counter-terrorism, while building a joint mechanism against drug smuggling and examining joint military and police training schemes.
The Turkish government has denied that it has not done enough against fighters based in the border regions, pointing out that the military has conducted operations there.
The three presidents also covered tensions between Pakistan and India, after New Delhi said that Pakistani nationals were involved in a series of attacks in Mumbai last week which left at least 171 people dead.
"We jointly condemn the Mumbai attacks," Gul said.
Pakistan is still waiting for "concrete proof" from India that Lashkar-e-Taiba, a Pakistan-based group was behind the attacks, Zardari said.
The trilateral meeting comes after an initial summit in Ankara in April 2007, in which Karzai and Pervez Musharraf, then president of Pakistan, said their governments would work together against fighters linked to the Taliban and al-Qaeda.