Traditional dancers were there to entertain the dignitaries and parents waiting to get their children vaccinated.
At least 3,000 people were in Homa Bay county in western Kenya for the launch.
Health Minister Sicily Kariuki addressed the gathering, saying the East African nation was excited to be part of the trial and urging parents to ensure their children received all four doses of the vaccine needed to provide protection.
The new RTS,S vaccine has been found to prevent malaria cases in four out of 10 children - between the ages of five and 17 months - as well as cut the most severe cases of malaria by a third.
It works by training the immune system to attack the malaria parasite, which is spread by mosquito bites.
Kenya aims to vaccinate at least 52 children per month until the end of the trial - that is more than 100,000 children over the next three years.