The visit, confirmed by China and North Korea, was Mr Kim's first known foreign trip since taking office in 2011.
He held "successful talks" with President Xi Jinping, China's Xinhua news agency reported.
China is North Korea's main economic ally and it was thought highly likely it would consult Beijing before planned summits with South Korea and the US.
Mr Kim is due to meet South Korean President Moon Jae-in in April, and US President Donald Trump in May.
The Beijing visit is considered a significant step in North Korea's preparation for the proposed talks.
What did the two leaders discuss?
Mr Kim arrived with his wife, Ri Sol-ju, by train on Sunday and left Beijing on Tuesday afternoon, according to reports.
During the visit, Mr Kim assured his Chinese counterpart he was committed to giving up his nuclear weapons, Xinhua reported, but with conditions.
"The issue of denuclearisation of the Korean Peninsula can be resolved, if South Korea and the United States respond to our efforts with goodwill, create an atmosphere of peace and stability while taking progressive and synchronous measures for the realisation of peace," Mr Kim was reported saying.
The North's conditions include the removal of a US nuclear guarantee for South Korea, observers say.
North Korea's KCNA news agency called the visit "a milestone" in improving bilateral ties.
Mr Kim's arrival and departure were shrouded in secrecy. China said the visit was "unofficial" - so there was no announcement of it in advance, prompting speculation about who was on the train when it was spotted arriving.
Because of the unofficial status of the visit, some of the normal protocols for foreign visits were not observed. For example no North Korean country flags were hung around the Great Hall of the People on Tiananmen Square.
Why is Kim's visit so significant?
It's the latest in a flurry of diplomatic activity since the start of the year sparked by the Winter Olympics in South Korea.
Relations between North Korea and China, historically strong, had been deteriorating, with China backing US moves to tighten international sanctions in response to the North's growing nuclear threat.
But China, a military giant over the border, is still responsible for virtually all of North Korea's food and fuel aid.
It has largely been an observer of the recent diplomatic moves by Pyongyang towards the US and South Korea.
"It makes sense for North Korea to explain their positions and co-ordinate with China, their most important partner," Andray Abrahamian, research fellow at Pacific Forum CSIS.
"Relations have been extremely strained the last five years and China has been sidelined in the diplomacy of the last several months," he said.
"From Beijing's perspective, this is a visit that should have happened some time ago."
To some extent, this is a "symbolic visit of courtesy" to China, Fyodor Tertitskiy of North Korea monitoring site NK News, said.
"They have two upcoming summits - one with Seoul and one with Washington - and they are probably interested in hearing the Chinese position as well."
KCNA also said Mr Xi had accepted an invitation to return the visit.
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