French soldiers have been fighting Islamic militants in the north of the former French colony since 2013.
He is due to review some of the 4,000 anti-insurgent troops France has deployed in the region.
This is Mr Macron's second foreign trip as president. He visited German Chancellor Angela Merkel in Berlin a day after his inauguration on Sunday.
As president, he is expected to continue his predecessor's policy regarding military presence in West Africa.
France retains a strong influence in its former colonies.
Mr Macron has talked about writing a new page in his country's relationship on the continent, and of breaking away from the old neo-colonial networks.
As a candidate, he stirred controversy at home by labelling France's colonial war in Algeria a crime against humanity - something which was well-received in the former colonies.