Craig Spencer works as a fellow of a international emergency medicine at New York Presbyterian Hospital
Dr Craig Spencer, who treated Ebola patients while working for the charity Medecins Sans Frontieres (MSF), came down with a fever on Thursday, days after his return, officials say.
He is the first Ebola case diagnosed in New York, and the fourth in the US.
Meanwhile, Mali has confirmed its first case of Ebola after a two-year-old girl tested positive for the virus.
More than 4,800 people have died of Ebola - mainly in Liberia, Guinea and Sierra Leone - since March.
Dr Spencer, 33, left Guinea on 14 October, and returned to New York City on 17 October via Europe. On Tuesday he began to feel tired and developed a fever and diarrhoea on Thursday.
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 the patient.
New York officials said Dr Spencer had travelled on the subway and gone out jogging before he started feeling unwell.
But 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. They added that those who came into contact with Dr Spencer were not at risk.
"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."
Quarantine
Mr 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.
Mr Cuomo said officials had identified four people with whom Dr Spencer had contact during the period in which he was potentially infectious.
His fiancee and two friends have been placed into quarantine, said Dr Mary Bassett, New York's health commissioner.
Dr Spencer is the fourth person to be diagnosed with the disease in the US.
The first caught Ebola in his native Liberia and travelled to Dallas, Texas, before his symptoms set in. He died on 8 October.
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.
The girl's mother died in Guinea a few weeks ago and the child was then brought by relatives to Mali, Reuters news agency quoted a health ministry official as saying.
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.
Symptoms of Ebola
Symptoms include high fever, bleeding and central nervous system damage
Spread by body fluids, such as blood and saliva.
Fatality rate can reach 90% - but current outbreak has mortality rate of about 70%.
Incubation period is two to 21 days.
There is no proven vaccine or cure.
Supportive care such as rehydrating patients who have diarrhoea and vomiting can help recovery.
Fruit bats, a delicacy for some West Africans, are considered to be virus's natural host.
Source: BBC News
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