The recommendation is based on results from an ongoing pilot programme in Ghana, Kenya and Malawi that has reached more than 800 000 children since 2019.
"This is a historic moment. The long-awaited malaria vaccine for children is a breakthrough for science, child health and malaria control," said WHO Director-General Dr Tedros Adhanom Ghebreyesus in a press release on Wednesday.
"Using this vaccine on top of existing tools to prevent malaria could save tens of thousands of young lives each year," he added.
Malaria remains a primary cause of childhood illness and death in sub-Saharan Africa. More than 260 000 African children under the age of five die from malaria annually.
In recent years, WHO and its partners have been reporting a stagnation in progress against the deadly disease.
"For centuries, malaria has stalked sub-Saharan Africa, causing immense personal suffering,” said Dr Matshidiso Moeti, WHO Regional Director for Africa.
"We have long hoped for an effective malaria vaccine and now for the first time ever, we have such a vaccine recommended for widespread use. Today’s recommendation offers a glimmer of hope for the continent which shoulders the heaviest burden of the disease and we expect many more African children to be protected from malaria and grow into healthy adults," she explained.