Kenya, Ghana and Malawi were chosen for the trial because all a high number of malaria cases, despite their strong prevention and vaccination programmes.
The malaria vaccine is called RTS, S and will be tested whether it will perform well in "real-life" conditions in Malawi, Ghana, and Kenya.
World Health Organization regional director for Africa Dr Matshidiso Moeti told the BBC: "The prospect of a malaria vaccine is great". It is said to be given four times to get its full effects: once a month for three months, then another dose 18 months after.
"The world's first malaria vaccine is a real achievement that has been 30 years in the making", said the chief executive of Gavi, Dr. Seth Berkley.
The researchers are conducting the testing to assess the effectiveness of the vaccine and also to determine the feasibility of the vaccine's delivery to the populations which are most at risk. The day was established to provide "education and understanding of malaria" and spread information on "year-long intensified implementation of national malaria-control strategies, including community-based activities for malaria prevention and treatment in endemic areas".
According to experts, it reflects the vision of a world without the disease, established in the World Technical Strategy against malaria 2016-2030.
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Even though it marks a major, promising milestone in the ongoing fight to eradicate the disease that killed 429,000 people in 2015, Mosquirix is not 100 percent effective. The organization made the announcement on the eve of World Malaria Day.
"There will be other vaccines which will be more efficient, but in the meantime, this will have a significant influence", she added.
But the United Nations agency has said in the past that such estimates are based mostly on modelling, and data is so poor for 31 countries in Africa - including those believed to have the worst outbreaks - that it could not tell if cases have been rising or falling in the last 15 years. Trials so far involving 15,000 participants from seven countries suggest RTS, S reduces the frequency of malaria episodes by 40 percent.
The injectable vaccine RTS, S developed by the British pharmaceutical giant GlaxoSmithKline (GSK) in partnership with the PATH Malaria Vaccine Initiative took decades of work and billions to develop.
"This is great news, actually", said Dr. Photini Sinnis, deputy director at the John Hopkins Malaria Research Institute, and on the first GSK scientists that worked on developing the vaccine, according to CNN.
Meanwhile, the development of a malaria vaccine has ramped up with a number of exciting candidates emerging of late, including one that can be delivering through the skin with a microneedle patch and another that injects live malaria parasites into the human body.