By lifting its nine-month-old declaration, the UN's health agency is acknowledging that Zika is here to stay.
The infection has been linked to severe birth defects in almost 30 countries.
These include microcephaly, where babies are born with abnormally small heads and restricted brain development.
The WHO says more than 2,100 cases of nervous-system malformations have been reported in Brazil alone.
Although the virus is mostly spread by mosquitoes, it can also be sexually transmitted.
Few people die from Zika and only one in five people infected is thought to develop symptoms. These can include fever, a rash and joint pain.
Dr David Heymann, the head of a WHO emergency committee on the virus, said it still posed a "significant and enduring" threat.
The WHO will now shift to a longer-term approach against the infection, which has spread across Latin America, the Caribbean and beyond.
Where did Zika come from?
It was first identified in monkeys in Uganda in 1947.
The first human case was detected in Nigeria in 1954 and there have been further outbreaks in Africa, South East Asia and the Pacific Islands.
Most were small and Zika has not previously been considered a major threat to human health.
But in May 2015 it was reported in Brazil and has since spread rapidly.
"Its current explosive pandemic re-emergence is, therefore, truly remarkable," the US National Institutes of Health said.