Health Minister Ousmane Kone made the announcement on Malian television, saying that the patient was a 2-year-old girl who had come from neighbouring Guinea, where the Ebola epidemic began last December.
The child was tested for the virus at a hospital Wednesday in the Malian town of Kayes, which is about 375 miles (600 kilometres) from the capital of Bamako.
"The sick child and the people who were in contact with her in Kayes were immediately identified and taken care of," Kone said.
Health officials have long viewed Mali as one of the most vulnerable to Ebola's spread as the nation borders Guinea — one of the hardest-hit countries — and Senegal.
The World Health Organization said Wednesday that Ebola now has killed at least 4,877 people and infected 9,936 across West Africa. Nearly all the cases and deaths, though, have occurred in three countries — Liberia, Sierra Leone and Guinea.
Like the reported case in Mali, neighbouring Senegal also had an imported case from Guinea. Senegal and Nigeria, though, both have now been declared Ebola-free after no new cases emerged after 42 days.