Hebner officiated matches for World Championship Wrestling (WCW) during much of the 1980's. He was the referee during the famous "I Quit" match at Starrcade 1985 between Tully Blanchard and Magnum T.A.. He could also be seen at ringside during the first ever WarGames match at the 1987 Great American Bash as well as the final match of the Bunkhouse Stampede tournament in January 1988.
Just days after that match, Hebner debuted in the World Wrestling Federation as a referee during a WWF Championship match pitting champion Hulk Hogan against challenger André the Giant, which aired live on February 5, 1988, on The Main Event. In the storyline, Hebner's identical twin brother Dave Hebner was the assigned official, but unbeknownst to Hogan, André's manager Ted DiBiase had bribed the then-unknown Earl Hebner to steal the victory and the championship. Earl then counted André's pin against Hogan, even though Hogan's shoulders were clearly off the mat. As André and DiBiase were celebrating (with André quickly "selling" his title to an overjoyed DiBiase), Dave (whom DiBiase had locked in a closet prior to the match) ran to the ring and confronted Earl. The two brothers argued, and they fought each other in the middle of the ring. Hulk Hogan, figuring out that Dave's "evil twin" had jobbed him out, picked Earl up and gorilla press slammed him over the ropes and onto the aisleway (missing DiBiase).
This match helped set up a 14-man elimination tournament at WrestleMania IV, since WWF President Jack Tunney declared the title "vacant" a week after The Main Event match as the WWF Championship "cannot be bought or sold," where the winner would win the WWF World Heavyweight Championship.
Meanwhile, the WWF continued to build heat for Earl Hebner through a kayfabe "investigative report" published in the promotions' flagship publication, WWF Magazine.
However, the "evil twin" referee storyline was quickly dropped when Dave was apparently injured in the aftermath of the Hogan-Andre Main Event match, forcing Dave out of action until after WrestleMania IV. The storyline was then shifted to have Earl come clean, and he was the referee when "Macho Man" Randy Savage won the tournament final at WrestleMania IV against "Million Dollar Man" Ted DiBiase for the WWF Championship.
The most infamous event in Hebner's career came during the main event of the 1997 Survivor Series in what has since been dubbed the “Montreal Screwjob”. During a match for the WWF World Heavyweight Championship between then-champion Bret Hart and challenger Shawn Michaels, Hebner signaled for the timekeeper to ring the bell (signifying the end of the match) while Michaels had Hart in a Sharpshooter hold, even though Hart visibly had not submitted. Michaels had thus "won" the WWF World Heavyweight Championship. Hebner had, at the behest of Vince McMahon, "screwed" Hart out of the title. The fallout of the screwjob led to a large degree of antagonism towards Hebner, McMahon, and Michaels, especially in Canada, where fans often chant "You screwed Bret!" at the offending parties.
Hebner was involved in several storylines. He spearheaded the referee's strike in 1999, resulting in referees being given the authority to defend themselves if physically provoked by wrestlers. In early 2000, he cost Triple H his WWF Championship by quick-counting during a match between Triple H and Chris Jericho following weeks of abuse by Triple H. Triple H eventually forced Hebner to reverse the decision, promising never to lay his hands on Hebner as long as Hebner was a WWF employee. After Hebner took the title from Jericho and gave it back to Triple H, Triple H "fired" Hebner and promptly Pedigreed him and beat him unconscious. Hebner was reinstated by Linda McMahon thirteen days later, replacing corrupt guest referee Shane McMahon during a title match between Triple H and The Rock at Backlash 2000 and counting the fall when The Rock covered Triple H for the pin. During the Invasion angle in late 2001, Hebner became involved in a feud involving WCW referee Nick Patrick. Patrick was a biased referee who often helped The Alliance achieve victories over their WWF opponents. Hebner defeated Patrick in a match at WWF Invasion.
On July 18, 2005, WWE announced that Hebner was released from the company.