WNYC-FM began regularly scheduled broadcasts on the FM band as W39NY on March 13, 1943, at 43.9 MHz, operating as the sister station to WNYC (AM).

Giuliani believed that broadcasting was no longer essential as a municipal service, and that the financial compensation from selling the stations could be used to help the City cover budget shortfalls.

WNYC-AM-FM's studios, in the nearby Manhattan Municipal Building, had to be evacuated and station staff was unable to return to its offices for three weeks.

WNYC-FM temporarily moved to studios at National Public Radio's New York bureau in midtown Manhattan, where it broadcast on its still operating AM signal transmitting from towers in Kearny, New Jersey and by a live Internet stream.

On June 16, 2008, NYPR moved from its 51,400 square feet (4,780 m2) of rent-free space scattered on eight floors of the Manhattan Municipal Building to a new location on Varick Street, near the Holland Tunnel.

WQXR's intellectual property (call letters and format) was acquired from the New York Times Company as part of a three-way transaction with Univision Radio.

Following the U.S. entry into World War II, then-mayor Fiorello H. La Guardia made use of the station every Sunday in his Talk to the People program.

During a lengthy newspaper workers strike, La Guardia also used the WNYC airwaves to read the latest comic strips to local youngsters while they were not available in New York.

Margaret Juntwait, an announcer and classical music host at WNYC for 15 years, left for the Metropolitan Opera in September 2006.