The Malian foreign ministry said Traore's "friendship and working visit" in the capital Bamako was scheduled to last around three hours.
The 34-year-old Burkinabe junta chief will meet his Malian counterpart, Assimi Goita, who came to power in a putsch in August 2020, they said.
"The main issue will be the fight against terrorism," a Burkinabe official said, referring to the two countries' bloody struggle against jihadists.
Traore ousted Lieutenant-Colonel Paul-Henri Sandaogo Damiba, who in January had toppled Burkina's last elected president, Roch Marc Christian Kabore.
Under Assimi Goita, who came to power in a putsch in August 2020, Mali began to weave closer ties with the Kremlin, acquiring aircraft to strengthen its beleaguered armed forces and bringing in Russian "trainers", described by Western countries as Wagner Group mercenaries.
As this relationship intensified, ties with Paris, Mali's traditional ally, deteriorated and France became a target of vilification.
Paris this year pulled out the last troops it had deployed in Mali under its Barkhane anti-jihadist force in the Sahel.
Burkina Fasio has been marked by anti-French protests in which some demonstrators have waved Russian flags and demanded the departure of a contingent of 400 French special forces.
On Sunday, the new prime minister, Apollinaire Kyelem de Tembela, hinted that Burkina may look at stronger connections with Russia, in the light of "the new deal" in security.