The action was the first time Kim had been included in Treasury sanctions.
In January, North Korea conducted its fourth nuclear test, followed up in February with the launch of a ballistic missile that successfully placed a satellite in orbit.
They also come a few weeks after Donald Trump, the Republican Party's presumptive presidential nominee, said he would meet with Kim to discuss North Korea's nuclear program.
Mark Toner, the State Department Deputy spokesman, also called on North Korea "to refrain from actions and rhetoric that further destabilize the region and focus instead on taking concrete steps toward fulfilling its commitments and worldwide obligations". "Against such considerations external pressure to punish for general human rights violations has little impact", he said.
The U.S. and North Korea do not have formal diplomatic relations, although they retain a channel of communication through the North's diplomatic mission at the United Nations in NY.
North Korea, one of the most isolated countries in the world, has always been under economic sanctions for its nuclear program.
US officials also acknowledge that the latest sanctions won't bring about any dramatic change.
Political prison camps across the reclusive state are estimated to hold between 80,000 and 120,000 detainees, including children.
"Lifting the anonymity of these functionaries may make them think twice from time to time when they consider a particular act of cruelty or repression", an anonymous senior Obama administration official was quoted as saying.
North Korea on Thursday lashed out at the move, calling it an "open declaration of war against DPRK" and "the worst crime that can never be pardoned", according to state news agency KCNA.
In March, both the UN Security Council and President Obama sanctioned the country in response to its nuclear and missile tests, but, as the Christian Science Monitor's Bamzi Banchiri reported in April, "North Korea has continued to be belligerent, underscoring various doubts that the sanctions wouldn't work". It is a sign that "there probably isn't much of a hope for a diplomatic resolution", said Zachary Goldman, a former policy adviser in the US Treasury's Office of Terrorism and Financial Intelligence. OFAC says any property or other assets held within US jurisdiction by those named on the list are frozen.
The North Korea mission to the United Nations did not respond to a request for comment. But senior administration officials said they had been long planned to take more aggressive actions that would move human rights violations - until now on the periphery of the United States' efforts to isolate and punish North Korea for its bad behavior - to a more central element of the administration's strategy.