"Today Mali has its first imported case of the Ebola virus," the ministry said yesterday in a statement. The girl was diagnosed after she arrived at a hospital in the western town of Kayes on Wednesday, it added.
The child and those she has come into contact with have been put in isolation. The identity of the infected girl was not released.
Health ministry spokesman Markatche Daou said that she had travelled to neighbouring Guinea with her grandmother and that the authorities were aware of her itinerary.
The ministry said the girl had visited Kissidougou, a town in the southern part of Guinea where the Ebola outbreak was first identified in December 2013.
"Everyone who had contact with the girl is under medical surveillance," he said.
The west African nations of Guinea, Liberia and Sierra Leone have borne the brunt of the deadly Ebola virus.
According to World Health Organization figures 10,000 people have been infected and almost 4,900 have died of the disease in west Africa.
Mali's health ministry said all necessary steps had been taken to avoid the spread of Ebola, and called on residents to remain calm.
However it warned against all unnecessary travel to affected areas and urged hygiene and safety measures to be respected.
In April there were some suspected Ebola cases in Mali, but these proved to be false alarms.
In August Senegal also registered a confirmed Ebola case, imported from Guinea. That case did not spread and last week Senegal was declared Ebola-free. International alarm has been stoked by cases beyond Africa.
Spain has seen one non-fatal infection, a nurse who caught Ebola from a patient she cared for -- a missionary who died of the disease after returning from Liberia.
In United States, two nurses fell ill after caring for a Liberian man who died from the disease on October 8, the first Ebola case to be diagnosed on US soil.
So far, though clinical trials are underway, no vaccine has been produced for the disease which is transmitted through bodily fluids, leaving health workers especially at risk.