He will meet with Pakistani President Pervez Musharraf, Prime Minister Mohammedian Soomro, and other officials.
Karzai, who arrived on Wednesday, is being accompanied by a delegation of over 50 Afghan officials, including the foreign minister, the finance minister, and the trade minister, as well as governors of provinces bordering Pakistan, and other officials.
The Afghan president last visited Islamabad in February 2006 to express sympathy and support for the country in the aftermath of a devastating October 2005 earthquake.
Relations between Pakistan and Afghanistan, Washington's principal allies in the region, remain cool.
Kabul accuses Islamabad of not doing enough to fight pro-Taliban groups based in Pakistan.
Pakistan denies the accusations.