World Health Organization said Ghana, Kenya and Malawi were chosen because they already run large programmes to tackle malaria, including the use of bed nets, yet still have high numbers of cases.
Nearly half of the world's population is at risk of malaria, but sub-Saharan Africa is disproportionately affected by the disease, which is spread by mosquitoes infected with a parasite.
The injectable vaccine, called RTS, S, was developed to protect children from malaria, and the vaccine will be incorporated into a complementary malaria tool, which if proven effective will be added into WHO-recommended measures to prevent the disease.
WHO Regional Director for Africa Dr Matshidiso Moeti said in a statement that the vaccine has the potential to save thousands of lives.
The vaccine consists of three injections administered over the course of three months, followed by a final booster dose 18 months later.
Pilot implementation strategy The three countries selected to participate in the pilot were based on the criteria of high coverage of long-lasting insecticidal-treated nets; well-functioning malaria and immunisation programmes - a high malaria burden even after scale-up of LLINs; and participation in the Phase III RTS, S malaria vaccine trial.
Almost 429,000 people died in 2015 from the mosquito-borne disease, a majority of whom were young children in Africa. In 2015, sub-Saharan Africa was home to 90 percent of malaria cases and 92 percent of malaria deaths. There are millions of people who still do not have access to the services they need to prevent and treat malaria, warned the source.More news: Chechen President: Eliminate All Gay Men By Ramadan
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It is understood that the vaccine will be tested on children between five to 17 months old to see whether its protective effects shown so far in clinical trials can hold up under real-life conditions.
There has been enormous progress in fighting the disease.
This is yet another solid front against a disease that has for years remained a major killer of children, women and men, taking a toll on productivity in the regions where it is endemic.
Africa is known to be the continent with the highest number of malaria cases. For more information look here What is the new vaccine?
Malaria episodes reduced by 40 per cent in tests on 15,000 people in seven countries over five years of clinical trials and could therefore save hundreds of thousands of lives. She argued that the data which was collected during the pilot program is bound to help the organization decide upon the wider use of the new vaccine.
A coalition of worldwide organizations and humanitarian groups including Gavi, the Vaccine Alliance, are bankrolling the pilot program's first phase, running from 2017 to 2020, for a price tag of $49.2 million.