Gérard Prunier was born in Paris and studied in France and the United States. After serving in the French Army, he emigrated to Canada and later traveled to Africa as a Canadian aid worker, serving in Uganda. He fled the country in 1972 during the fighting which followed the attempt to overthrow Idi Amin Dada. He then became a political refugee in Tanzania, where he survived by driving trucks. After traveling widely throughout Eastern Africa for several years, Prunier returned to Europe and completed a Ph.D. on the expulsion of Asians from Uganda, which he had witnessed in 1972.
Prunier joined the Centre National de la Recherche Scientifique (CNRS) in 1984 and wrote extensively on East African contemporary history and politics, with a particular focus on conflicts. Over the past 30 years he has written 170 articles and eight books in four languages.
Prunier worked as Director of the Centre Français des Etudes Ethiopiennes in Addis Ababa between 2001 and 2006. He retired from CNRS at the end of 2009 and became a political and business consultant on East and Central African matters. He is a fellow of the Atlantic Council, and his next work will be a history of statelessness in Somalia since the fall of the Siad Barre regime.