He will address French soldiers stationed in the city of Gao in Mali's deeply troubled north. The French base there has 1,600 soldiers -- the biggest outside the country.
The troops are part of Operation Barkhane, a French counterterror operation whose mission is to target jihadist groups operating in the Sahel region south of the Sahara Desert.
Set up in 2014, the operation comprises around 4,000 soldiers who are deployed across five countries -- Mauritania, Mali, Niger, Chad and Burkina Faso. It operates Mirage 2000 fighter jets and drones for gathering intelligence.
Macron will hold talks with Malian counterpart Ibrahim Boubacar Keita on the fight against terrorism and the west African country's rocky path to normality since a 2015 peace deal.
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Northern Mali fell to jihadist groups linked to Al-Qaeda in March 2012, and these forces were driven out of key towns by a French-led military intervention the following year.
But jihadists continue to roam the country's north and centre, mounting attacks on civilians and the army, as well as French and UN forces still stationed there.
Sources in his entourage said the 39-year-old Macron would seek to emphasise the need for closer European cooperation in the fight against jihadists, especially with EU heavyweight Germany.
France wants a "new Franco-German impetus so that Europe plays a greater role in defence and security matters, especially in Africa and the Sahel," a source said.
Macron has already discussed this on Monday with German Chancellor Angela Merkel, the first leader he met after taking office.