Karzai is accompanied by members of his core policy group that includes the foreign minister, national security advisor and his chief of staff, the Afghan embassy said.
Iranian President Mahmoud Ahmadinejad is expected to arrive later in the day for the summit being hosted by Pakistan President Asif Ali Zardari.
Shortly after his arrival, Karzai held one-on-one and delegation-level talks with Prime Minister Yousuf Raza Gilani.
The Pakistani delegation included army chief Gen Ashfaq Parvez Kayani, Defence Minister Chaudhry Ahmed Mukhtar, Foreign Minister Hina Khar and Interior Minister Rehman Malik.
Strategy for Afghanistan after withdrawal of US troops, the bilateral meetings and the trilateral summit are expected to focus on the regional security situation, particularly the reconciliation process in Afghanistan and Iran's tensions with Israel over its controversial nuclear programme.
The war on terrorism and efforts to counter drug trafficking and crimes too are expected to figure in the talks, officials said.
The Iran-Pakistan gas pipeline project will figure in talks between Zardari and Ahmadinejad.
Minister for States and Frontier Regions Engineer Shaukatullah, senior officials and Afghan diplomats received President Zardari on his arrival at a military airbase.
Karzai will also meet Zardari for bilateral talks, officials said. This is Karzai's second visit to Pakistan in eight months.
He last visited Islamabad in June, weeks after the US Special Forces killed Osama bin Laden in a raid in the garrison town of Abbottabad.
Karzai's visit marks the revival of high-level contacts between Pakistan and Afghanistan for the reconciliation process, including efforts to bring the Afghan Taliban to the negotiating table.
These contacts were suspended following the assassination of Afghan peace envoy Burhanuddin Rabbani in September.
Afghan officials had blamed the assassination on elements based within Pakistan.
During the trilateral summit, the three presidents will have two sessions, one this evening and another on Friday.
A joint communique will be issued at the conclusion of the summit, which will also discuss economic issues.
Though a meeting of the three presidents was scheduled for November last year, it could not be held in the wake of Rabbani's assassination.
Afghanistan had refused to attend the summit in October when Ahmadinejad proposed a meeting to bring Afghan and Pakistan leaders to the negotiation table in the wake of Rabbani's killing.
Image: Pakistan PM Gilani shows Afghanistan President Karzai way to a photo opportunity before their meeting in Islamabad on Thursday
Photograph: Faisal Mahmood/Reuters
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