Burkina's Lieutenant-Colonel Paul-Henri Sandaogo Damiba and Mali's Colonel Assimi Goita have agreed to "better examine and strengthen" their military partnership.
"The two countries... intend to pool their efforts in the fight against terrorism", the statement said.
The announcement came during Damiba's visit to Bamako - his first since seizing power in January.
The Malian presidency confirmed the news in a separate statement.
Damiba and Goita also discussed the contingent of Ivorian soldiers currently detained in Mali accused of being mercenaries, the Burkinabe presidency said.
On Saturday, Mali released three women among 49 soldiers held since July.
Damiba declined to comment publicly on the dispute. He is expected Monday in Abidjan.