The $59,000 (Ksh5.9 million) award is the third of eight prizes handed out annually by a foundation named for Crown Princess Leonor.
"By means of this initiative, it has been possible to reach the most vulnerable and remotest populations that would not have regular access to health services, in particular, thanks to its flying doctors piloting light aircraft-ambulances," the jury said in a statement.
The organisation was also recognized for developing distance training programmes to strengthen local capacities in the fight against AIDS, tuberculosis and malaria.
"Its efforts to eradicate female genital mutilation via social and cultural awareness-raising actions are also worthy of note," the jury added.
Based in Nairobi, Amref was founded in 1957 as the Flying Doctors of East Africa and claims to be the oldest and largest indigenous African health organisation.
One of its employees, Nice Nailantei Leng'ete, an activist against female genital mutilation, has just been named one of Time magazine's top 100 most influential people in the world.
The $59,000 (Ksh5.9 million) award is the third of eight prizes —also including arts, social sciences and sports— handed out annually by a foundation named for Crown Princess Leonor.