Pate, a medical doctor trained in internal medicine and infectious disease, will take over the helm on August 3 from US medical epidemiologist Seth Berkley, in charge since 2011, Gavi said in a statement.
Gavi, which has been at the forefront of efforts to immunize the world against Covid, had conducted a year-long recruitment process to find a replacement for Berkley.
Pate, in his 50s, "stood out in a field of world-class candidates," said Jose Manuel Barroso, chair of the Gavi board and a former European Commission president, who headed the search.
The Nigerian doctor served as the state minister of health in his country from 2011 to 2013, during which time he lead an initiative to revive routine vaccinations and primary health care, introduced new vaccines to the country and chaired a presidential taskforce to eradicate polio.
He served as the World Bank's global director for health and director of its global financing facility between 2019 and 2021, leading the bank's $18-billion Covid response.
Pate, who is currently serving as the Julio Frenk Professor of Public Health Leadership at Harvard Chan School of Public Health, said in Monday's statement that he was "deeply honored to be joining Gavi," which he described as "one of the most impactful organizations in global health."
The Gavi vaccine alliance is a non-profit organization created in 2000 to provide an array of vaccines to developing countries.
It says that since its inception, it has provided vaccines to more than 981 million children, "and prevented more than 16.2 million future deaths, helping to halve child mortality in 73 lower-income countries."
Gavi has taken the lead on the Covax initiative, alongside the World Health Organization and the Coalition for Epidemic Preparedness Innovations.
The global scheme has so far shipped nearly 1.9 billion Covid vaccines to 146 territories, with the focus on providing donor-funded jabs to the 92 weakest economies.