WNYU is run entirely by university students. It plays a diverse array of music and encourages independent artists to submit their work for airplay. Their website features archives of aired shows, allowing listeners to tune into missed broadcasts.

The offices and studios are located at 5-11 University Place in Greenwich Village. WNYU's main transmitter is located at University Heights in the Bronx, the former location of NYU. Another transmitter is licensed as WNYU-FM1, a co-channel booster station located at University Plaza at the current campus 40°43′37″N 73°59′53″W, and serving lower Manhattan where the main signal is blocked by the skyscrapers of upper Manhattan.

The frequency of 89.1 in the New York metropolitan area is actually reserved by the Federal Communications Commission (FCC) for the United Nations (to a maximum of 20 kW effective radiated power at up to 500 feet (152 m) HAAT, per 47 CFR §73.501. This is the only allotment in the country to be specified in the reserved band used by non-commercial educational stations. Because this was never used by the U.N., WNYU and WFDU were allowed to broadcast on it, on a shared time basis.

WNYU has been home to Plastic Tales from the Marshmallow Dimension as well as the legendary New Afternoon Show since 1980, when programmer Sal LoCurto flipped the format from progressive rock to new wave, creating a U.S. launching pad for an entire new generation of music including The Human League, Heaven 17, R.E.M., Public Image Limited as well as NYC and Hoboken acts such as The dB's, The Fleshtones, The Bongos, Liquid Liquid, KONK, ESG, The Individuals and The Bush Tetras.

The original New Afternoon Show line-up included Gary Cee (now Director of Operations at Clear Channel TriState in Sussex, New Jersey), Naomi Regelson, Michael "Pablo" Dugan, Sal LoCurto, and Evan "Funk" Davies. Brian "Weems" Williams replaced Gary Cee in 1981. Loscalzo (later of WPDH, WRCN, WDRE, KROQ-FM and K-Rock/NY replaced Evan "Funk" Davies in 1982. Other New Afternoon Show DJs during the 80's included Hrynyszyn, Jon Fox, Anne Clark, Sylvia, and Hugh Foley.

The station broke ground by airing one of the first hardcore punk programs - "Noise! The Show" - with host (and future MTV veejay) Tim Sommer. A snippet of this show can be heard on the Beastie Boys collection "Some Old Bullshit". Following the success of "Noise! The Show", a similar punk and hardcore radio show called "Crucial Chaos" started in the late 1980s and was a staple of the NYHC scene. An infamous live set from the show with an on-air fight between members of Sick of it All and Born Against still exists and can be found on the internet. Crucial Chaos continues to this day, now in its 24th year and still features live sets and interviews from bands in the current hardcore scene.

Alec Baldwin was a frequent guest on short-lived comedy program "Comedy Hell" hosted by Max Keiser who would later go on to invent the Hollywood Stock Exchange and appear as a presenter on both Al-Jazeera English and BBC World News. The show was co-hosted and produced by Loscalzo.

Current programming

Current WNYU DJs include DJ Eclipse of Non Phixion, who hosts a hip-hop show called The Halftime Show every Wednesday night, Tim Sweeney, whom Time Out New York named "one of the most in-demand DJs in the city" in an April 2005 feature, spins dance classics and new electronic music on Beats In Space, Tuesday nights. The Village Voice facetiously called Beats In Space the "Best Radio Show for Hearing 'Disco Train' Several Times on Repeat" in their Best of 2005 issue.

"The Cheap Seats," a sports talk program, airs each Monday night. The show airs for one half hour and aims to break down professional sports from a uniquely independent viewpoint, especially focusing on teams from the New York region. Listeners may call in and offer their own opinions on the air. The show is currently hosted by members of WNYU's News Department. Other past members include Kenny Albert (Fox), John Schmeelk (New York Giants), Aaron Goldhammer (ESPN Radio), Brook Silva-Braga (HBO), Jay Cowit (WNYC), Rachel Steinberg, Bryan Koch, Keith Sabalja, Rob Maiale, and Brad Clough. Hosts often interview relevant figures from the world of sports. Past guests have included DeMaurice Smith, John Sterling, Kerry Rhodes, Satch Sanders, Ramses Barden and Stu Jackson. The WNYU sports department also provides coverage of NYU men's and women's basketball.

"Tunnel One", which airs every Tuesday evening from 9:00pm to 10:30pm EST, is New York City's only weekly Jamaican ska, rocksteady, and foundation reggae & dancehall radio program. Begun circa 1997, and hosted by djMush1 (trumpet player/multi-instrumentalist, engineer, arranger, and producer, and formerly of the Slackers and Murphy's law, and currently of The Hungry March Band, The Scorchers, & Al Paragus record label and event space [home of When Dance Was Nice]), Tunnel One has featured live in-studio guests such as Junior Reid, Carlton Livingston, Clive Chin, Johnny Osbourne, Danny Dread (Stereo Mars/Volacano), Jah Wise (Tippatone), Tony Screw (Downbeat), Junior Cat, General Trees, Professor Nuts, Al Campbell, Brigadier Jerry, Monty Alexander, Welton Irie, Ranking Trevor, Ranking Joe, and many more.