Malaysian Prime Minister Najib Razak said a coroner had approved the release of Kim Jong Nam's body.
Kim was murdered at Kuala Lumpur airport with a lethal nerve agent last month.
The assassination led to a major diplomatic dispute between Malaysia and North Korea.
Malaysia has not directly blamed North Korea for the killing, but there is widespread suspicion that Pyongyang was responsible.
Meanwhile, nine Malaysians who had been barred from leaving North Korea returned to Malaysia early on Friday. They include three embassy staff and six family members.
The Malaysian prime minister had also said that all North Koreans would be allowed to leave Malaysia.
BBC South East Asia correspondent Jonathan Head says that probably includes three North Koreans who are wanted by Malaysian police in connection with the killing.
Malaysia expressed outrage earlier this month over what it described as North Korea holding its citizens hostage. But now it appears to have acceded to North Korea's wishes to get those Malaysians released, our correspondent adds.
A video circulated by Japanese media later on Thursday reportedly showed two of the suspects - an embassy employee and a worker for the North Korean state airline - on a plane, and cargo said to be Kim's casket.
Najib said: "I had a deep personal concern about this matter, and we worked intensively behind the scenes to achieve this successful outcome.
"Many challenges were overcome to ensure the return of our fellow Malaysians."
He added: "The government believes strongly in the principles of justice and sovereignty. Our police investigation into this serious crime on Malaysian soil will continue.
"I have instructed for all possible measures to be taken to bring those responsible for this murder to justice."


