France's new president also reaffirmed his commitment to helping the West African country, where French soldiers have been facing extremists since 2013.
Mr Macron said he hoped to strengthen ties with Germany to boost security in the area, according to Reuters.
This trip is Mr Macron's second foreign visit since his inauguration on Sunday.
He has already visited German Chancellor Angela Merkel in Berlin.
Mr Macron arrived in Gao, in the north of the former French colony, just before 10:00 GMT (11:00 BST) on Friday.