Boubacar will be transferred to the United Arab Emirates in a medical plane. He will stop over in a neighboring country, which was not specified.
On Tuesday, the former president was hospitalized after suffering a mild stroke-like attack. Hours earlier he had got permission from the military junta that led the coup to travel outside the country.
"The trip to the Arab Emirates has a medical purpose. Boubacar will have tests to determine the causes of the stroke," the former president's representatives said.
Specialists estimate that this could be the beginning of the overthrown president's exile outside the country.
On August 18, Boubacar and several officials of his government were arrested after the coup d'état. They were released a week later thanks to the mediation of the Community of West African States (ECOWAS).
Boubacar and other officials of his dissolved government could face justice for crimes of corruption.
Besides political instability, Mali suffers from inter-community violence and frequent jihadist attacks against the Libyan Army and other foreign forces deployed in large areas of the African country.
African refugees from Somalia, Nigeria and Mali are fleeing to Latin America. They are risking everything to find a safe passage to the U.S. pic.twitter.com/K13MJT3nbX