The patients are a Burkinabè couple who recently returned from France in February, Health Minister Claudine Lougue told reporters.
The man is 73-years-old and the woman is 57. They tested positive for the virus on Monday and have been placed in isolation, authorities say.
A third person who was reportedly in close contact with the couple has been placed under observation.
Burkina Faso becomes the sixth sub-Saharan African country to report positive tests for coronavirus.
Latest figures indicate there are now 100 confirmed coronavirus cases across.