Dr. Craig Spencer, who treated Ebola patients while working for the charity Medecins Sans Frontieres (MSF), came down with a fever on October 23, days after his return, officials say.
He is the first Ebola case diagnosed in New York, and the fourth in the US.
More than 4,800 people have died of Ebola – mainly in Liberia, Guinea and Sierra Leone – since March.
Dr. Craig Spencer, 33, left Guinea on October 14, and returned to New York City on October 17 via Europe. On October 21 he began to feel tired and developed a fever and diarrhea on October 23.
He immediately contacted medical services and was taken to the city’s Bellevue Hospital, where he is being kept in isolation.
President Barack Obama said his thoughts and prayers were with Craig Spencer.
New York officials said Dr. Craig Spencer had travelled on the subway and gone out jogging before he started feeling unwell.
At a news conference late on Thursday, they sought to ease fears of an outbreak in the densely populated city of 8.4 million people, saying officials had prepared for weeks for an Ebola case.
“There is no reason for New Yorkers to be alarmed,” Mayor Bill de Blasio said.
“Ebola is an extremely hard disease to contract. New Yorkers who have not been exposed to an infected person’s bodily fluids are not at risk.”
Governor Andrew Cuomo said: “We can’t say that this is an unexpected circumstance.”
President Barack Obama telephoned both the mayor and the governor to discuss the deployment of health officials and to offer “any additional federal support necessary”, the White House said.
Ebola patients are only infectious if they have symptoms, and the disease is only transmittable through bodily fluids, experts say.
Andrew Cuomo said officials had identified four people with whom Dr. Craig Spencer had contact during the period in which he was potentially infectious.
His fiancée and two friends have been placed into quarantine, said Dr. Mary Bassett, New York’s health commissioner.
Dr. Craig Spencer is the fourth person to be diagnosed with the disease in the US.
The first patient, Thomas Eric Duncan, caught Ebola in his native Liberia and travelled to Dallas, Texas, before his symptoms set in. He died on October 8.
Two nurses who treated him in Dallas subsequently came down with the disease and are recovering in hospital.
Meanwhile, on Thursday the West African country of Mali confirmed its first Ebola case – a two-year-old girl recently returned from Guinea.
Mali is now the sixth West African country to be affected by the latest Ebola outbreak – however Senegal and Nigeria have since been declared virus-free by the WHO.
Separately, the World Health Organization (WHO) has already identified at least two experimental vaccines which it believes could be promising.
At a meeting in Geneva, the UN health body said it wanted tests of the vaccines to be completed by the end of December.
The WHO says 443 health workers have contracted Ebola, of whom 244 have died.
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