Kim Jong-Nam was killed with the lethal nerve agent VX on February 13 in a Kuala Lumpur airport, triggering a diplomatic row between Malaysia and North Korea, which expelled each other's ambassadors and barred their citizens from leaving.
But a deal announced by Malaysian Prime Minister Najib Razak and confirmed by North Korean state media on Thursday said the two countries would lift their respective travel bans, and Kuala Lumpur would send the body to North Korea.
"Following the completion of the autopsy on the deceased and receipt of a letter from his family requesting the remains be returned to North Korea, the coroner has approved the release of the body," Najib said in a statement.
Najib did not specify who in the family had made the request. Kim's wife and children, who were living in exile in the Chinese territory of Macau, staged a vanishing act after the murder and are believed to be in hiding.
The nine Malaysians prevented from leaving North Korea "have now been allowed to return to Malaysia", he said, declaring later on Twitter that the "diplomatic crisis is over".
Watch: Malaysia's Foreign Minister discusses release of nine Malaysian citizens from North Korea
"They took off from Pyongyang today at 7:45 pm (1145 GMT) Malaysian time, and will land in Kuala Lumpur (Friday) around 5:00 am," he said in the statement that referred to Kim as "the deceased" rather than by name.
North Korean citizens in Kuala Lumpur will also be allowed to return home under the deal.
The North's state-run news agency KCNA said the two countries also agreed to discuss the "re-introduction of the visa-free" entry system that existed before the spat.
South Korea has blamed Pyongyang for the Cold War-style killing, citing what they say was a standing order from North Korea's leader Kim Jong-Un to murder his exiled and estranged half-brother.
But the North denies this and denounced Malaysia's investigation into the death as an attempt to smear the secretive regime.
It had insisted that the man died of a heart attack and his body should be handed over to Pyongyang.
A van believed to be carrying the body of Kim left a hospital morgue in Kuala Lumpur Thursday, where it had been kept for more than six weeks, and headed for the airport's cargo centre.
Chinese and Malaysian media reported it was put on board a Malaysian Airlines plane bound for Beijing that left Kuala Lumpur at 7:39 pm.
An AFP photographer saw a North Korean embassy van and officials leaving Beijing airport early Friday morning.
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Analysts said the North Korean regime may use Kim's body as a "propaganda tool".
"They will likely use the body to claim they were not responsible and tell an alternative narrative," said Bridget Welsh, an expert on Southeast Asian politics.
Pyongyang has refused to confirm the identity of the victim, who was carrying a North Korean passport bearing the name of Kim Chol when he was killed.
Malaysia however has officially confirmed his identity using DNA evidence and had said it had been waiting for his next of kin to claim the body.
There are fears Kim's 21-year-old son, Kim Han-Sol, could be targeted next.
Two women -- one Vietnamese and one Indonesian -- have been arrested and charged with the murder. Airport CCTV footage shows them approaching the 45-year-old victim and apparently smearing his face with a piece of cloth.
Malaysian investigators are also seeking seven North Korean suspects, four of whom left Malaysia on the day of the murder. Interpol has issued an international arrest warrant for the four men.
Malaysia's police chief has said he believes they fled to Pyongyang while the other three are hiding in North Korea's embassy in Kuala Lumpur.
