In a statement on Sunday, the WHO praised “the Egyptian government and people” for their efforts to “end a disease that has been present in the country since ancient times”.
It said Egypt was the third country to be certified in the WHO’s Eastern Mediterranean Region, following the United Arab Emirates and Morocco.
Globally, 44 countries and one territory have reached this milestone.
But the WHO said the certification was only “the beginning of a new phase”, urging Egypt to be on the alert to preserve its malaria-free status.
To get the WHO certification, a country must demonstrate the capacity to prevent the re-establishment of transmission.
The UN public health agency said first efforts to limit human-mosquito contact in Egypt began in the 1920s when it banned rice cultivation and agricultural crops near homes.
Malaria is caused by a complex parasite which is spread by mosquito bites.
Vaccines are now being used in some places – but monitoring the disease and avoiding mosquito bites are the most effective ways to prevent malaria.