The president had made his intentions clear in late May, accusing the WHO of being under China's control in the wake of the coronavirus pandemic.
Despite calls from the EU and others, he said he would pull out of the UN agency and redirect funds elsewhere.
He has now notified the UN and Congress of his intentions, although the process could take at least a year.
Stéphane Dujarric, spokesman for the UN secretary-general, confirmed the US had notified it of its withdrawal, effective as of 6 July 2021.
Senator Robert Menendez, the leading Democrat on the Foreign Relations Committee, also wrote on Twitter: "Congress received notification that POTUS officially withdrew the US from the WHO in the midst of a pandemic.
"It leaves Americans sick and America alone."
A senior US administration official told CBS News that Washington had detailed the reforms that it wanted the WHO to make and engaged with it directly, but that the WHO had refused to act.
"Because they have failed to make the requested and greatly needed reforms, we will be today terminating our relationship," the official was quoted as saying.
Joe Biden, who will challenge Donald Trump in the November presidential election, tweeted: "On my first day as President, I will rejoin the WHO and restore our leadership on the world stage."
The US is the global health agency's largest single contributor, providing more than $400m (£324m; €360m) in 2019, around 15% of its total budget.
Under a Congress resolution in 1948, the US can withdraw but must give a year's notice and should pay outstanding fees, although it is unclear where Mr Trump stands on that. Mr Dujarric stressed that those conditions should be met.
The withdrawal will call into question the WHO's financial viability and the future of its many programmes promoting healthcare and tackling disease.