The note signalled a possible improvement in their strained relationships, which has soured over Pyongyang's growing weapons ambitions even though Beijing is its longtime ally and economic benefactor.
Xi's message, dated yesterday, was sent in response to congratulations from Kim last week for securing a second term as the head of China's ruling party.
"I wish that under the new situation the Chinese side would make efforts with the DPRK side to promote the relations between the two parties and the two countries to sustainable soundness and stable development," Xi said, according to the North's KCNA news agency said, addressing Kim as "Comrade Chairman".
The last time KCNA reported a message from Xi was in July 2016.
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Analysts say that such exchanges have become extremely rare under the current leaders, even though Beijing and Pyongyang traditionally sent greetings and congratulations on each other's key anniversaries in the past.
Their relationship was forged in the blood of the Korean War, when Mao Zedong sent millions of "volunteers" to fight US-led United Nations forces to a standstill.
But Beijing has grown increasingly frustrated by its belligerent neighbour, and rapidly backed a new set of UN measures after a flurry of missile launches by the North and its sixth nuclear test in September.
Professor Yang Moo-Jin of the University of North Korean Studies in Seoul said the public exchange of messages signalled a willingness on both sides to improve relations.
"If the message was more intimate, we could expect a faster thawing of ties," he added, "but for now, it shows that both sides agree on the need to improve their relations".
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