Cape Verde, an archipelago of 10 islands in the central Atlantic Ocean, has faced severe epidemics in densely populated areas before it implemented targeted interventions.
"(It) gives us hope that with existing tools, as well as new ones including vaccines, we can dare to dream of a malaria-free world," WHO Director-General Tedros Adhanom Ghebreyesus said in a statement.
The WHO said that in the heavily affected African region, Cape Verde had become the third country after Mauritius and Algeria to eliminate the mosquito-borne disease.
It joins the ranks of 43 countries and one territory certified by the WHO.
"This (certification) has the potential to attract more visitors and boost socio-economic activities in a country where tourism accounts for approximately 25% of GDP," the statement said.
The WHO certification is granted when a country has demonstrated no locally transmitted cases of malaria in at least the last three years.