The license-holder is WNET.org, formerly known as the Educational Broadcasting Corporation. WNET is also the parent of the Long Island-based PBS station WLIW (channel 21) and the operator of the New Jersey PBS network NJTV.

Independent station

WNET commenced broadcasting on May 15, 1948, as WATV, a commercial television station owned by Atlantic Television, a subsidiary of Bremer Broadcasting Corporation. Bremer also owned two northern New Jersey radio stations, WAAT (970 AM, now WNYM) and WAAT-FM (94.7 MHz., now WNSH). The three stations were based in the Mosque Theatre (now Symphony Hall) at 1020 Broad Street in Newark. WATV was the first of three new stations in the New York City television market to sign on the air during 1948, and was also the first independent station. One unusual daytime program, Daywatch, consisted of a camera focused on a teletypewriter printing wire service news stories, interspersed with cut-aways to mechanical toys against a light music soundtrack. Another early series by the station was Stairway to Stardom (1950-1951), one of the first TV series with an African-American host.

On October 6, 1957, Bremer Broadcasting announced it had sold its stations for $4.5 million to National Telefilm Associates (NTA), an early distributor of motion pictures for television. On May 7, 1958, channel 13's callsign was changed to WNTA-TV to reflect the new ownership; the radio stations adopted these call letters as well. NTA's cash resources enabled WNTA-TV to produce a schedule of programming with greater emphasis on the people and events of New Jersey, in comparison to the other commercial television stations. NTA also sought to make channel 13 a center of nationally syndicated programming and produced several such entries, notably the anthology drama series Play of the Week; the talk show Open End, hosted by David Susskind; children's show The Magic Clown; and a popular dance program emceed by Clay Cole. But WNTA-TV continued to lag behind New York's other independent stations - WNEW-TV (channel 5, now WNYW), WOR-TV (channel 9, now WWOR-TV), and WPIX (channel 11) - in terms of audience size, and NTA incurred a large debtload. National Telefilm Associates put the WNTA stations up for sale in February 1961.

Transition

At least three prospective purchasers expressed interest in WNTA-TV. The most prominent was the New York City-based group Educational Television for the Metropolitan Area (ETMA), a consortium of businesspeople, cultural leaders and educators. ETMA believed that the non-commercial frequency that the Federal Communications Commission (FCC) allocated to the city, UHF channel 25, would not be nearly adequate enough to cover a market that stretched from Fairfield County, Connecticut in the north to Ocean County, New Jersey in the south. Prior to 1964, when the FCC required television manufacturers to include UHF tuners in newer sets as per the All-Channel Act, most viewers could not view UHF stations except with an expensive converter; only a few manufacturers made sets with built-in UHF tuning. Even for those who could access UHF stations, reception was marginal even under the best conditions.

With assistance from the University of the State of New York, ETMA had attempted to purchase channel 13 and convert it into a non-commercial station in 1957, when Bremer Broadcasting first put the station on the block; this bid was later withdrawn. This time ETMA was competing with NTA founding president Ely Landau, who had resigned from the company in order to head his own venture for this; and by David Susskind, who received financial backing from Paramount Pictures.

ETMA's initial bid of $4 million was rejected by NTA, but the citizens' group remained persistent. With the support and guidance of National Educational Television (NET) already in their pocket, ETMA later received an endorsement from newly appointed FCC chairman Newton Minow, who established public hearings to discuss the fate of channel 13. The pendulum quickly shifted in favor of channel 13 going non-commercial, and the private firms withdrew their interest.

On June 29, 1961, ETMA agreed to purchase WNTA-TV for $6.2 million. About $2 million of that amount came from five of the six remaining commercial VHF stations (WPIX was the lone holdout), all of whom were pleased to see a competitor eliminated. In addition, CBS later donated a facility in Manhattan to ETMA and NET for production uses. The FCC approved the transfer in October, and converted channel 13's commercial license to non-commercial.

"Tonight, you join me in being present at the birth of a great adventure." Edward R. Murrow, on the first broadcast of WNDT on September 16, 1962. The outgoing New Jersey governor, Robert B. Meyner, addressing state lawmakers' concerns over continued programming specific to New Jersey, and fearing the FCC would move the channel 13 allocation to New York City, petitioned the United States Court of Appeals on September 6, 1961, to block the sale of WNTA-TV. The court ruled in the state's favor two months later.

The unsettled deal almost caused National Telefilm Associates to reconsider its decision to sell the station altogether, and NTA made plans to go forward: WNTA-TV made a play to acquire broadcast rights for the New York Mets baseball team for its inaugural 1962 season. But faced with either consummating the transaction or seeing it cancelled, ETMA settled their differences with New Jersey officials on December 4, 1961. After a few last-minute issues arose to cause further delays, the transfer became final on December 22. Later that evening, WNTA-TV signed off for the final time. ETMA and NET then went to work converting the station, which they said would return with its new format within three months.

Ten months later, channel 13 was ready to be reborn. With legendary CBS reporter Edward R. Murrow at the helm on the maiden broadcast, ETMA – now the non-profit Educational Broadcasting Corporation – flipped the switch to WNDT (for "New Dimensions in Television") on September 16, 1962. The return of channel 13 as WNDT gave the New York City market its first educational station, and with a dial position on the coveted VHF band (in many other cities, including large ones, educational stations had to make do with UHF frequencies). New York's non-commercial UHF channel, on the other hand, signed on as WNYE-TV four-and-a-half years later in April 1967. Richard Heffner was appointed as WNDT's first general manager, serving in that position in its first year; Heffner continued to appear on channel 13 as producer and host of the public affairs program The Open Mind until his death in December 2013.

Educational station

During the transition, and after the inaugural broadcast, WNDT faced an immediate crisis. The American Federation of Television and Radio Artists (AFTRA) was concerned about the use of teachers – some of whom were union-certified performers – on non-commercial television, and how they would be compensated should their work be distributed nationally.

AFTRA called a strike on the morning of WNDT's debut. Engineers and technicians who were members of the International Brotherhood of Electrical Workers refused to cross the AFTRA picket line, leaving the station's management and other non-union employees to produce the three-hour inaugural broadcast. Immediately afterwards, channel 13 went off the air again, as the strike continued for nearly two weeks. The striking workers returned WNDT to the air after ten days, and on September 28, the labor dispute was settled. But the station's financial resources were drained, requiring an infusion of cash from the Ford Foundation to help keep the station running.

NET originally wanted to merge its operations with WNDT, which would have given the station a direct line of funding as well as make channel 13 NET's flagship station. The Ford Foundation, which supported both groups, stopped the proposed mergers on at least two different occasions (in 1962 and 1965).

Events that began in 1967 led the Ford Foundation to change its stance and push for a WNDT-NET merger. The newly formed Corporation for Public Broadcasting (created by an act of the United States Congress) initially supported NET's network role, while providing government funding for programming. But that move was followed two years later with the establishment of the Public Broadcasting Service as the CPB's own distribution system – which was a direct threat to NET's territory. It has been intimated that the CPB's creation was an attempt to curb NET's production of controversial documentaries and replace it with a less controversial, government-friendly broadcaster, less hostile in particular to the Johnson, and later the Nixon administrations (NET ignored the demand and continued on with the production of the critically acclaimed documentaries). At one point, President Nixon, frustrated with NET's documentaries criticizing his administration, especially its handling of the Vietnam War, almost managed to cut NET's $20 million funding grant in half. As a result, this led both Ford and the CPB to threaten NET with funding withdrawal in early 1970, unless it merged with the station. Not long after, Ford brokered the merger of WNDT and NET, which took effect on June 29, 1970. Channel 13's callsign was changed to the present WNET on October 1, 1970. NET ceased network operations three days later, though WNET continued to produce some shows for the national PBS schedule with the NET branding until about 1972.

Following the merger, David Loxton established the TV Lab in 1972 with support from the Rockefeller Foundation and New York State Council on the Arts. TV Lab provided artists with equipment to produce video pieces through an artist-in-residence program. The Independent Documentary Fund and Video Tape Review series were both produces of TV Lab. TV Lab ended in 1984 when the Corporation for Public Broadcasting withdrew funds.

Channel 13's studios and offices were originally located in the Mosque Theater at 1020 Broad Street in Newark, with transmitter on First Mountain in West Orange, New Jersey. For a short time studios were located at the Gateway Center office building in Newark. The station eventually moved its operations to Manhattan in 1982 and was based on West 58th Street in the Hudson Hotel, while retaining the Gateway Center studios for a few more years. In 1998, it moved to 450 West 33rd Street, straddling the railroad tracks going into Pennsylvania Station. The Associated Press and numerous other media groups have headquarters in the same building.

450 West 33rd Street, the former broadcast facility for WNET; also home to the New York Daily News and the Associated Press. Channel 13's transmitter facilities, including a newly installed digital transmission system, were destroyed on September 11, 2001, when airplanes hijacked by terrorists crashed into the north and south towers of the World Trade Center. Gerard (Rod) Coppola, channel 13's head transmitter engineer, was among those who perished when the north tower collapsed. His remains were discovered on December 25, 2001. For the next ten months WNYE-TV, headquartered in Brooklyn, became WNET's surrogate transmitter and airwave: for those without cable, repeats of WNET's prime-time schedule were broadcast on WNYE. Some time later, in February 2003, WNET completed its merger with Long Island PBS broadcaster WLIW (licensed to Garden City and based in Plainview), combining the two stations into one operation. While most of the two stations' operations have been merged, they still have separate studio facilities, separate governing boards, and conduct separate fundraising efforts.

During 2009, WNET's parent company, WNET.org, sustained financial difficulties, and in January, the company pared its workforce from 500 employees to 415, due to severe problems with its budget and fundraising. In October, WNET announced that its studios at 450 West 33rd Street would soon be up for sale, as it no longer needed the extra space. In November, WNET announced that all WNET.org employees would take an unpaid furlough for three to five days between Christmas and New Year's Day, with a skeleton crew of engineers remaining during that time to keep the stations on the air; however, they, too, would have to go on furloughs at the start of 2010. In 2011, WNET moved its studios and offices to Worldwide Plaza.

In 2014 The Tisch WNET Studios at Lincoln Center were built at the southwest corner of 66th and Broadway, this versatile, state-of-the-art facility houses two television studios. The space can also accommodate lectures, screenings and intimate concerts.

The new facility is named in honor of James S. Tisch and his wife, Merryl H. Tisch, whose $15 million gift is the single largest donation from individuals in WNET's nearly 50-year history.

On July 1, 2011, WNET took over the programming of the New Jersey Network, which was relaunched as NJTV. The network features increased coverage of news and issues pertinent to New Jersey, as well as programming from the WNET and PBS libraries. The transfer of programming to WNET was part of Governor Chris Christie's plan for the New Jersey government's exit from public broadcasting. As part of the deal, WNET airs NJTV's nightly statewide newscast, NJTV News, to meet its local programming obligations since it still operates on a frequency allocated to Newark. Previously, it had aired NJN's newscast, NJN News, which it co-produced with NJN.

Analog-to-digital conversion