The final few dozen patients are scheduled to be released by the end of the day.
A little more than 1000 patients were treated at the massive facility over the last month.
The Army Corps of Engineers set up the sprawling site inside the country's biggest convention center at the end of March.
Now that New York appears to be past the peak of the pandemic, the Javits Medical Center will close - but this facility and the other three military-run field hospitals in the area won't be broken down yet.
Key FEMA equipment and supplies will remain in case there is second wave of coronavirus.
"Just being able to actually leverage our technology and our skills to this situation has been amazing, and just the cooperation between the forces is absolutely incredible," said one medic we spoke to. "So I'm actually very fortunate to be in a position to help the way we are."
The 68-bed tent field hospital set up by Samaritan's Purse in Central Park to help fight the coronavirus pandemic is expected to close in the coming weeks as well.
Military staff at the Javits Center are expected to depart New York City beginning next week for redeployment.
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