Li's plane was escorted by six fighter jets of the Pakistani air force when it entered the country's airspace, reported Xinhua.
The Chinese premier was warmly welcomed at the airport by Pakistani President Asif Ali Zardari and interim Prime Minister Mir Hazar Khan Khoso.
Li, accompanied by Pakistan's top leaders, inspected the guard of honour, with a military band playing the national anthems of the two countries.
Pakistan is the second leg of Li's first overseas trip since he assumed Chinese premiership in March. Li left Mumbai earlier in the day after concluding a visit to India.