The "hypocritical and self-serving" body "makes a mockery of human rights", said US envoy to the UN Nikki Haley.
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 her country'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.
On Monday Mr Hussein has called the policy "unconscionable".
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