The “hypocritical and self-serving” body “makes a mockery of human rights”, said US envoy to the UN Nikki Haley.
Ms Haley last year accused the council of “chronic anti-Israel bias” and said the US was reviewing its membership.
Formed in 2006, the Geneva-based council has been criticised for allowing countries with questionable human rights records to be members.
But activists said the US move could hurt efforts to monitor and address human rights abuses around the world.
Ms Haley announced the US’s intention to quit the council at a joint news conference with Secretary of State Mike Pompeo, who called the council “a poor defender of human rights”.
UN Secretary-General António Guterres, in a statement released through his spokesman, responded by saying he would have “much preferred” the US to remain in the council.
The UN human rights commissioner, Zeid Ra’ad Al Hussein, called the US withdrawal “disappointing, if not really surprising, news”. Israel, meanwhile, has praised the decision.
The move comes amid intense criticism over the Trump administration’s policy of separating child migrants from their parents at the US-Mexico border.
The UN set up the council in 2006 to replace the UN Commission on Human Rights, which faced widespread criticism for letting countries with poor human rights records become members.
A group of 47 elected countries from different global regions serve for three-year terms on the council.
The UNHRC meets three times a year, and reviews the human rights records of all UN members in a special process the council says gives countries the chance to say what they have done to improve human rights, known as the Universal Periodic Review.
The council also sends out independent experts and has set up commissions of inquiry to report on human rights violations in countries including Syria, North Korea, Burundi, Myanmar and South Sudan.
The decision to leave the body follows years of US criticism.
The country initially refused to join the council in 2006, arguing that, like the old commission, the UNHRC had admitted nations with questionable human rights records.
It only joined in 2009 under President Barack Obama, and won re-election to the council in 2012.
But human rights groups voiced fresh complaints about the body in 2013, after China, Russia, Saudia Arabia, Algeria and Vietnam were elected members.
This followed Israel’s unprecedented boycott of one of the council’s reviews, alleging unfair criticism from the body.
Last year, Nikki Haley told the council it was “hard to accept” that resolutions had been passed against Israel yet none had been considered for Venezuela, where dozens of protesters had been killed during political turmoil.
Israel is the only country that is subject to a permanent standing agenda item, meaning its treatment of the Palestinians is regularly scrutinised.
On Tuesday, despite her harsh words for the UNHRC, Ms Haley said she wanted “to make it crystal clear that this step is not a retreat from our human rights commitments”.