This appears to be the first time that any country's human rights situation has been scheduled for ongoing debate by the UN's most powerful body.
China and Russia protested the move, the boldest effort yet to confront Pyongyang over the issue.
An angry North Korea, now on the defensive against a US accusation of hacking, has said it would refuse to recognise yesterday's meeting.
International pressure has built this year on Pyongyang after a UN-backed inquiry found grounds to believe that crimes against humanity have been committed under policies "established at the highest level of the State for decades."
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In a letter to Kim, the commission also warned that he could be held accountable."
North Korea accuses the United States and its allies of using the human rights issue as a weapon to overthrow its leadership. It also calls the dozens of people who fled the North and aided the commission of inquiry "human scum."
North Korea already sent a sharp warning last month, threatening further nuclear tests after the UN General Assembly's human rights committee voted to move the issue to the Security Council, which can take binding actions on matters of international peace and security.
The council has had North Korea's nuclear program on its agenda for years, but yesterday's meeting opens the door to wider discussion of abuses alleged in the recent inquiry, including starvation and a harsh political prison camp system of up to 120,000 inmates. Pyongyang rejects the inquiry's findings but never allowed it into the country.
UN Secretary-General Ban Ki-moon told reporters yesterday that he was closely following the Security Council's actions.
"Human rights should be given the highest priority" in any country," said Ban, who is South Korean.