The "jirgagai [mini-jirga] would be instrumental in shaping up the ways to tackle rising militant violence", Farooq Wardag, the deputy chairman of the Afghanistan Jirga Monitoring Commission, was quoted as saying by the Associated Press news agency.
State media said the meeting will form a committee to forward proposals to the two countries' governments.
"Both Afghanistan and Pakistan are faced with terrorism and together they need to face the challenge," Shah Mehmood Qureshi, Pakistan's foreign minister, said at the start of the session.
"Today Pakistan is more committed than ever not to allow anybody to use its territory for activities against any other country."
Qureshi vowed that al-Qaeda would be expelled but at the same time the "sovereignty of Pakistan will be protected at all cost."
The leader of the Afghan delegation, Abdullah Abdullah, the former foreign minister, said terrorism was a global challenge but "unfortunately both countries are at its centre".
"Both are moving together to meet the challenge," he said.
Violence has soared on both sides of the border, with Washington and Kabul urging Islamabad to tackle Taliban "safe havens" in Pakistan's tribal belt. Pakistan has also suffered a wave of suicide attacks.
Tribesmen on the Pakistani side have recently set up a number of tribal armies to counter the growing Taliban influence in the area, while Pakistani troops launched a two-month operation in the Bajaur tribal region in August.
Kamal Hyder, Al Jazeera's correspondent in Islamabad, said: "Political analysts will tell you that both the governments do not have their people's support.
"The beleaguered government of [President Hamid] Karzai is already facing problems in Afghanistan, and the new government in Pakistan has not been able to reduce the level of violence in the country.
"The war on both sides has dislocated a lot of people."