The filing comes just four months before the 75-year-old restaurant is to hand over its license to another operator.
Tavern Chief Executive Jennifer Oz LeRoy blames the filing on the financial crisis and New York City's decision to give the Tavern license to a new operator, according to The New York Times.
The new license was granted to Dean J. Poll, who runs the Central Park Boathouse restaurant.
The federal bankruptcy filing lists 20 creditors.
Poll, who takes over Jan. 1, plans to renovate with green technology. The original building, which dates to the 19th century, housed sheep.
LeRoy's father, Warner, took over the Tavern in 1976. He died in 2001.