WCTX is available on channel 9 on almost all of Connecticut's cable systems, this is reflected in the station's on-air branding "MyTV9". Like sister station WTNH, WCTX has a large Fairfield County audience as well. This area is part of the New York City television market, which is where MyNetworkTV flagship WWOR-TV is based. WCTX is considered an alternate ABC affiliate, airing that network's programs when WTNH is unable to do so such as during extended breaking news coverage or a local special.

'As early as 1953, a construction permit for the analog UHF channel 59 allotment was issued by the Federal Communications Commission (FCC) and was originally owned by the Connecticut Radio Foundation. However, the group was never able to get the station on-the-air and sold the permit to Impart Systems in 1967. In 1971, the then-owner of NBC affiliate WHNB (channel 30) built a low-power translator on UHF channel 59 in New Haven (W59AA licensed to West Haven). Although WHNB had boosted its power to cover New Haven a few months earlier, some areas in Southern Connecticut still could not get a good signal from the station.

On April 3, 1995 the station finally began broadcasting as a WB affiliate under the callsign WTVU under a local marketing agreement (LMA) with LIN TV, owner of WTNH. Before WTVU's sign on, The WB's programming had been shown on WTNH following its late newscast on Saturday nights (The WB only offered two hours a week of programmimg at that point).

The LMA also allowed WTVU to broadcast strong syndicated programs, mostly barter shows and second runs from WTNH. It also ran classic sitcoms and drama shows such as Perry Mason, I Love Lucy, Happy Days, The Honeymooners, The Andy Griffith Show, The Beverly Hillbillies, I Dream of Jeannie, Bewitched and Gilligan's Island among others that were removed from the schedules of WTXX (channel 20, now WCCT-TV) and WTWS (channel 26, now WHPX-TV) some years back. It also picked up the rights to telecast Hartford Whalers hockey games, which aired on the station until the team became the Carolina Hurricanes in 1997.

On April 1, 1996, the station changed its call letters to WBNE (for "WB New England"). After Tribune Broadcasting (a minority owner of The WB) purchased then-UPN affiliate WTXX, WBNE and that station swapped network affiliations on January 1, 2001. With the new network relationship came the current WCTX calls and use of the on-air identity "The X". That identity was used in lieu of the conventional "UPN (channel number)" branding. LIN TV purchased WCTX outright in 2002. On September 19, 2005, WCTX became known as "UPN 9," highlighting its cable channel position in some areas. This branding was the same as WWOR in New York City, a station that is available over-the-air and on cable in Southwestern Connecticut.

On January 24, 2006, CBS Corporation and the Warner Bros. Entertainment unit of Time Warner announced that UPN and The WB would cease broadcasting and merge their programming inventories to create a new network called The CW. WTXX was chosen as Connecticut's CW affiliate after its owner Tribune announced a ten-year deal with the upcoming network leaving WCTX to tentatively become an independent station once again. However on April 26, WCTX announced it would join MyNetworkTV (a second new network launched by News Corporation).

MyNetworkTV began broadcasting on September 5, and as a result, the station did not carry the final two weeks of UPN programming. With its new network affiliation, the station changed its branding to the current "MyTV9". As of the 2007/2008 season, University of Connecticut men's college basketball games now air primarily on WCTX while a handful of games air on sister station WTNH. It recently signed a multi-year television deal with the WNBA's Connecticut Sun to broadcast select regular season games as well.

Until March 31, 2008, WCTX served as the default MyNetworkTV affiliate on Charter Communications cable systems for the Springfield/Holyoke, Massachusetts market as that area did not have an affiliate of its own. On that date, ABC affiliate WGGB-TV added the network as a secondary affiliation on its new Fox-affiliated second digital subchannel. WCTX is still seen on Charter. WCTX was also repeated on W11BJ (now WFXQ-CD) from a transmitter on Rattlesnake Mountain in Farmington from 2004 until 2006 while LIN TV built a new transmitter for that channel and moved its city of license to Springfield.

On March 21, 2014, Media General announced that it would purchase LIN Media and its stations, including WTNH and WCTX, in a $1.6 billion merger. The merger was completed on December 19.

WCTX began airing sports programming from the American Sports Network on August 30, 2014]

Analog-to-digital conversion

WCTX shut down its analog signal, over UHF channel 59, on June 12, 2009, as part of the federally mandated transition from analog to digital television. The station's digital signal remained on its pre-transition UHF channel 39, using PSIP to display WCTX's virtual channel as 59 on digital television receivers, which was among the high band UHF channels (52-69) that were removed from broadcasting use as a result of the transition.

Newscasts

Since the start of the local marketing agreement with WCTX in 2000, WTNH has been producing a nightly prime time newscast at 10 p.m. on channel 59. It has competed right from its April 17, 2000 debut with WTIC-TV's 10 p.m. broadcast which established itself as the leading primetime newscast in the market since it debuted in 1989. As of the February 2008 ratings period, WTIC's weeknight newscast is actually the most watched late evening news broadcast in the market even gathering more viewership that the 11 p.m. newscasts on Connecticut's Big Three stations.