Gates -- one of the world's richest men -- is the latest in a string of Western business leaders to visit China since the country ended strict Covid controls that largely closed it off from the world for almost three years.
The visit is Gates' first to China in four years, and included a rare sit-down between the Chinese head of state and a foreign business leader.
"You are the first American friend I have met in Beijing this year," Xi told Gates in Beijing, according to the state-run People's Daily.
"We have always placed our hopes on the American people, and hoped for continued friendship between the peoples of the two countries," Xi added.
Gates, in turn, said he was "very honoured to have this chance to meet", according to a recording of the meeting shared by state broadcaster CCTV.
"We've always had great conversations and we'll have a lot of important topics to discuss today," he said.
"I was very disappointed I couldn't come during these last four years, and so it's very exciting to be back."
A state media readout also quoted Gates as praising China's efforts in "tackling the Covid-19 pandemic, setting a good example for the world".
- $50 million -
The meeting comes ahead of an expected visit to China by US Secretary of State Antony Blinken on Sunday.
It also follows an announcement by the Bill and Melinda Gates Foundation on Thursday that it would give $50 million to support Chinese efforts to fight malaria and tuberculosis.
The foundation announced it would renew a collaboration with the Global Health Drug Discovery Institute (GHDDI) -- a Beijing-based group set up by Gates, the Beijing municipal government and Tsinghua University.
The $50 million will support "efforts to improve health outcomes worldwide through lifesaving therapies for infectious diseases such as tuberculosis and malaria, which disproportionately affect the world's poorest", the Gates Foundation said in a statement.
On Thursday, Gates gave a speech at GHDDI, the Gates Foundation said, hailing China's efforts in eradicating malaria and poverty reduction.
"China has made significant gains reducing poverty and improving health outcomes within China," Gates said.
"I'm hopeful China can play an even bigger role in addressing the current challenges, particularly those facing African countries."
Gates last visited China in 2019, where he met with first lady Peng Liyuan to discuss his foundation's work in HIV/AIDS prevention.
During a visit to the country the previous year, he brandished a jar of human waste at a forum in Beijing in a bid to draw attention to the shortage of toilets in the developing world.
A string of American business leaders have visited China this year, talking up their optimism about its vast market and trade ties between the two economic powerhouses.
JPMorgan Chase CEO Jamie Dimon visited China in recent weeks, as did Tesla CEO Elon Musk, who made his first visit in more than three years.
Musk, who has extensive business interests in China, met senior officials in Beijing and visited Tesla's Gigafactory on the outskirts of Shanghai for a late-night meeting with staff.
In March, Apple CEO Tim Cook visited Beijing, saying his company enjoyed a "symbiotic" relationship with China.
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