The Dubai-based carrier said flights to the Guinean capital of Conakry were suspended beginning Saturday until further notice.
Guinea, along with neighbouring Liberia and Sierra Leone, is struggling to contain an outbreak of the disease that has sickened more than 1,300 people and killed more than 700 since March.
Emirates' rapid growth has turned its Dubai base into one of the world's busiest air hubs, funnelling travellers around the globe.
The airline will continue flying to the West African nation of Senegal, which borders Guinea, saying it "will be guided by the updates from international health authorities."
The International Air Transport Association last week said it is working with the World Health Organization and the International Civil Aviation Organization to monitor potential fallout for air travel from the outbreak, and that the WHO is currently not recommending travel restrictions.