Li left India, which was the first stop on a four-country tour with Switzerland and Germany ahead in the itinerary.
He arrived in Islamabad when Pakistan, for the first time since its founding in 1947 has completed democratic elections, although there is yet no let up in the militant and sectarian violence that has damaged the economy. This is the first democratic change of leadership in Pakistan, which for more than half of its history has been ruled by its military.
Li is to meet with Nawaz Sharif, leader of the Pakistan Muslim League PML-N party, who, after an impressive election victory, is set to become prime minister for the third time. His second term as prime minister was cut short in 1999 after a military coup led by Gen. Pervez Musharraf, who is under house arrest on various charges.
Li's two-day visit is crucial as it comes when Sharif will have his hands full repairing the economy. China and Pakistan have strengthened their political, economic, defense and strategic ties over the years much to the concern of neighboring India.
China's official Xinhua News Agency said Li's visit to Pakistan "is expected to cement the "all-weather' partnership between the two countries."
Earlier, Chinese Vice Foreign Minister Song Tao said Beijing hops the visit will "send positive signals to the people of both countries and the international community that China values its relations with Pakistan and is committed to inheriting the traditional friendship and expanding the mutually beneficial cooperation between the two sides."
A report by Pakistan's state-run news agency, carried in the country's Daily Times, said Li's visit "is of much significance as the leadership of two countries will focus on broadening the horizons of multifaceted ties enjoyed by the two friendly nations, which stood triumphant against all challenges."
Dawn newspaper said topics to be covered in talks between Li and Pakistani leaders would include neighbor Afghanistan and the withdrawal of coalition troops from that county.
"It is important to note that China relies on Pakistan's input and perspective on regional issues," the report quoted a Pakistani diplomat as saying.
Li is also to meet with Pakistani President Asif Ali Zardari and other officials.
The two sides will sign a number of documents for close cooperation in various fields.
Li's India visit appears to have been well-received. Being the representative of China's new and reform-minded leadership, his trip was closely watched.
China and India have had rocky relations since they fought a brief border war in 1962. Li's trip was preceded by a tense situation last month stemming from a border incident in the Ladakh region of the Himalayas in which India charged China had set up tents in Indian territory, an allegation China denied. India also moved troops to the area.
The standoff ended after both sides withdrew but the incident again pointed to the prevailing tensions over unresolved border disputes going back to 1962.
Li's visit to India got extensive coverage in the official Chinese media, with Xinhua noting Beijing's new leadership "prioritizes enhancing ties with New Delhi despite border spats and other disputes."
Xinhua said leaders in both countries have realized the "world has sufficient room for the development of China and India and the two neighbors share vast common interests, despite their lingering border issues and the much-hyped China-India rivalry for regional primacy."
Both countries promised to increase trade to $100 billion by 2015 but India remains concerned about the growing trade imbalance and wants greater access to Chinese markets for Indian products.
Li acknowledged India's concerns and promised to help Indian companies find access China's market. He also expressed confidence about mitigating the trade imbalance, saying China has no intention to run a trade surplus.
Prior to leaving India, Li, in a speech on his vision for bilateral relations, assured his audience neither country is a threat to the other, the Times of India reported.
A joint statement called for the development of an economic corridor among Bangladesh, China, India and Myanmar.
The Hindu newspaper in an editorial said the decision by the two sides to encourage their special representatives on the boundary question to push forward negotiations towards a mutually acceptable settlement "will hopefully breathe political life into a process that is at a virtual standstill despite 15 rounds of talks."