Adnan Abu Walid al-Sahrawi formed Islamic State in the Greater Sahara (ISGS) in 2015.
The group is blamed for most attacks in the region, including the targeted killing of French aid workers in 2020.
Mr Macron called Sahrawi’s death “another major success in our fight against terrorist groups in the Sahel”.
The Sahel is a vast, three million sq km (1.16 million sq miles) area that stretches across Africa south of the Sahara desert, from Senegal in the west to Somalia in the east.
Macron did not disclose the location or any details of the operation.
French Defence Minister Florence Parly tweeted that Sahrawi died after a strike by France’s Operation Barkhane force, which fights Islamist militants in the Sahel, mostly in Mali, Niger, Chad and Burkina Faso.
She added that it was “a decisive blow against this terrorist group”, and that the “fight continues”.