Dr Craig Spencer was working for the humanitarian organization in Guinea, one of three West African nations hardest hit by Ebola.
Spencer, 33, developed a fever and gastrointestinal symptoms and notified Doctors Without Borders on Thursday morning, the organization said in a statement.
Spencer was transported to Bellevue Hospital from his Manhattan apartment by a specially trained team wearing protective gear, the New York City Department of Health and Mental Hygiene said in a statement.
He tested positive for Ebola, the Times said, making him the city's first diagnosed case.
The Times said a further test will be conducted by the U.S. Centers for Disease Control and Prevention to confirm the initial test.
Mayor Bill de Blasio and New York Governor Andrew Cuomo planned a news conference at the hospital for 9 pm ET (0100 GMT).
A spokeswoman for the mayor said she could not confirm or deny the report and declined to comment ahead of the news conference.
Americans' fears about Ebola, which has killed nearly 4,900 people, largely in Liberia, Sierra Leone and Guinea, have mounted since the first person diagnosed with it in the United States, a Liberian man who had flown to Texas, was hospitalized in Dallas last month.
The man, Thomas Eric Duncan, died on Oct. 8, and two nurses who treated him became infected with the virus. A task force has been set up following missteps in handling the case.
Spencer's Facebook page, which included a photo of him clad in protective gear, said he went to Guinea around Sept. 18 and then flew to Brussels on Oct. 16.
He has specialized in international emergency medicine at Columbia University-New York Presbyterian Hospital in New York City since 2011, according to his profile on the LinkedIn career website.
Columbia in a statement said he has not been to work nor seen any patients since his return.
The health department said earlier in the day that it was tracing all of the patient's contacts to identify anyone who may be at potential risk.
Spencer's Facebook page, which included a photo of him clad in protective gear, said he went to Guinea around Sept. 18 and then flew to Brussels on Oct. 16.
He has specialized in international emergency medicine at Columbia University-New York Presbyterian Hospital in New York City since 2011, according to his profile on the LinkedIn career website.
Columbia in a statement said he has not been to work nor seen any patients since his return.
Before Spencer was admitted to Bellevue, the staff spent about three hours shutting off certain areas to isolate the seventh-floor ward where he would be kept, one nurse aide said.
Spencer's apartment in Manhattan's Harlem neighborhood was sealed off on Thursday but the rest of the six-story brick building remained open to residents, health officials said.
The virus is spread through direct contact with bodily fluids from an infected person and is not airborne.
The United States this week began requiring travelers coming from Liberia, Sierra Leone and Guinea to enter through one of five airports conducting increased screening for the virus. It also is directing those travelers to check in with health officials every day and report their temperatures and any Ebola symptoms for 21 days.
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