Long debuted in the WWF as a referee in 1999 at the Royal Rumble and stayed with that role until September 2002, when he was taken off the road. Like his previous referee stints, Long went by the shortened Teddy Long name during this period. He was a referee at the Over The Edge 1999 PPV, during the match after Owen Hart's tragic death: a mixed tag match between Jeff Jarrett/Debra and Val Venis/Nicole Bass. Long was the referee when Darren Drozdov ended up paralyzed and can be seen in WWE's Don't Try This At Home warning looking at the paramedics lift Droz up on a stretcher.
He was re-packaged as a villainous manager once again under his full name, and perhaps his most notable managing stint in this period came when managing D'Lo Brown, Rodney Mack, Christopher Nowinski, Rosey, Mark Henry and Jazz at different times, telling fans to "get Down wit' da Brown" and to "Back da Mack." When he was drafted to SmackDown!, he managed Mark Jindrak.
After Kurt Angle was fired from the General Manager position in July 2004, Long became the new and first African-American General Manager of SmackDown!. Long immediately turned face on his first night as GM when he fined Angle $5,000 for not having his wrestling gear with him. Because of his face turn, his new position saw him giving the fans what they wanted and making matches that put villains at disadvantages, notably JBL, a stark contrast to other WWE managers, such as Eric Bischoff and Mr. McMahon, who would blatantly favor heels. At first, he continued use of his "Hate-orade" talk, but less aggressively, and with humor. One example was when he stripped Booker T of the US Championship for "drinkin' Hate-orade." Long would also introduce the New Talent Initiative during this time, which saw the likes of Bobby Lashley and Mr. Kennedy debut in 2005 and MVP in 2006, among others. The New Talent Initiative would continue when Long moved to ECW in 2008 and would see the debuts of Kofi Kingston, Evan Bourne, Braden Walker, Ricky Ortiz, Gavin Spears, and Jack Swagger.
Theodore Long still had problems with Booker T and his defense of the United States title, however, as Booker T attempted to get out of title defenses on a number of occasions by pretending to be injured, and having other wrestlers fight on his behalf. Eventually, Long got tired of these shenanigans, and at No Way Out 2006, Booker was told to face Chris Benoit or be stripped of the US title. Benoit won the match and was congratulated by Theodore Long.
After Randy Orton had cheated to obtain Rey Mysterio's title shot at WrestleMania 22, Long placed Mysterio back in the match and made it a Triple Threat match, at the same time warning Orton that he could still remove Orton from the match if he disobeyed Long.
At Judgment Day 2006 Long fired Melina and Johnny Nitro from SmackDown!. On the following SmackDown!, JBL suffered the same fate after losing the United States Championship to Bobby Lashley, and then losing a World Heavyweight Championship match to Rey Mysterio in his Judgment Day rematch.
On the September 4, 2006 episode of Raw, Long appeared to a tremendous ovation in his hometown. During a six-person, intergender tag match between Randy Orton, Edge, and Lita against Trish Stratus, Carlito, and John Cena, some fans chanted Theodore's name.
In April 2007, Long became the on-screen boyfriend of Kristal Marshall, after weeks flirting with each other backstage. Long then began to look for an assistant so he could spend more time with Kristal, eventually revealing Vickie Guerrero as his new assistant on May 25, 2007, an appointment made partly at Kristal's request. On the June 22, 2007 episode of SmackDown!, Long asked Kristal to marry him. Kristal ran out of the ring, crying, but later agreed to marry him. On the July 27, 2007 episode of SmackDown!, Ron Simmons was named the best man for "Theodore Rufus Long" and Kristal's wedding on the September 21, 2007 episode of SmackDown! emanating from Long's hometown of Atlanta, Georgia. The wedding was not completed, however, due to constant disruptions and Long having a heart attack just as he started to say "I do". He then fell in to a coma. The storyline never finished out as planned as Marshall left the WWE shortly afterwards due to creative differences. Long returned on the November 30, 2007 episode of SmackDown! as the Assistant General Manager and made a match at Armageddon for the World Heavyweight Championship. He started to feud with Guerrero over her position as the General manager as she continued to favour Edge. On May 16, 2008, Long quit his role of Assistant General Manager.
On the June 3, 2008 episode of ECW, it was announced that Long had become the new General Manager of the ECW brand by order of the WWE Board of Directors.
On the April 7, 2009 episode of ECW, Long announced he was returning to SmackDown! as General Manager, with Tiffany replacing him on ECW. By doing this, he became the first person in the history of the company to have a second term as General Manager. He made his official TV return to SmackDown! on April 10, when he announced that the Hardys Matt and Jeff would face each other in the first ever stretcher match in SmackDown history.
At the Breaking Point PPV, Long restarted the World Heavyweight Championship match between CM Punk and the Undertaker after Undertaker made Punk submit using his Hell's Gate submission finisher, stating that the ban on the maneuver was still in effect. On the September 18, 2009 episode of Friday Night Smackdown, WWE Chairman Mr. McMahon instructed Long to go down to the ring and explain his actions regarding the conclusion of the World Heavyweight Championship Submission match between champion CM Punk and The Undertaker in which he (Long), as well as referee Scott Armstrong and CM Punk played key roles in recreating the infamous Montreal Screwjob at Breaking Point (held at the Bell Centre in Montreal, Quebec, Canada), site of the 1997 fiasco. This time, with The Undertaker being the target of a planned conspiracy. As he returned from the ring to the back stage area, he entered his waiting limousine only to be kidnapped by The Undertaker, who was in the driver's seat. The following week on SmackDown Long was brought into the arena inside a coffin by Undertaker's druids where he again legalized Undertaker's Hell's Gate submission hold. Teddy Long made a guest appearance on RAW and later Shawn Michaels performed his finishing maneuver [Sweet Chin Music] on Teddy Long after Long refused to draft him to SmackDown. He then began a feud with Drew McIntyre, the first part of which revolved around McIntyre qualifying for the Money in the Bank ladder match at WrestleMania XXVI, which was instead won by Jack Swagger. On the 7th May episode of Smackdown, after McIntyre brutally assaulted Matt Hardy, Long stripped McIntyre of his Intercontinental Championship and fired him. As a result, the Intercontinental Championship was vacant. Thus, Long issued the Intercontinental Championship tournament involving Christian, Kofi Kingston, Cody Rhodes and Dolph Ziggler. However, after Kingston emerged victorious against Christian, Long was issued a letter from Vince McMahon reinstating McIntyre and forcing Kingston to give his title back to McIntyre. He then made a match for McIntyre's Intercontinental Championship at Over the Limit against Kofi Kingston.
On the May 28 episode of SmackDown, Long read a letter from Mr. McMahon's office given to him by Drew McIntyre which stated that Matt Hardy was suspended until further notice after Matt attacked McIntyre at the Over the Limit PPV event and told Matt not to go near McIntyre and if he did so, Long would be fired as the General Manager of SmackDown.
On the June 11 episode of SmackDown!, a frustrated Drew McIntyre announced a match between Long and McIntyre would take place the following week on Smackdown per orders of Mr. McMahon. Drew said if Long didn't compete, he would be fired. McIntyre then went on to win the match the following week, after it was ordered that Long had get down on his knees, proclaim Drew as "The Chosen One" and then lay on his back and let McIntyre pin him without a fight. The next episode of SmackDown!, Long reinstated Matt Hardy into the SmackDown! brand and made Drew McIntyre compete against the returning Matt Hardy. Hardy would win the match, but after the match, Long came out and told McIntyre that his work visa had expired, and made security carry him out of the arena. On the July 9 edition of SmackDown, McIntyre was reinstated and pleaded forgiveness from Long, even going so far as to nominate Long as a member of the WWE Hall of Fame as well as get on his knees and proclaim Long "the best boss he ever had." Long, however, did not believe him and announced a Money in the Bank qualifying match (for the upcoming Money in the Bank pay-per-view) against Kofi Kingston.
On January 21 episode of Smackdown, Long was found (kayfabe) unconscious in his office, suffering a head injury. He returned on the February 18 episode of Smackdown, where he revealed Vickie Guerrero and Dolph Ziggler to have attacked him. He then scheduled a match between the new World Heavyweight Champion Ziggler and Edge. Edge would win the match, becoming a eleven-time world champion. After the match, Long would then fire Ziggler. The following week, he fired Vickie Guerrero after she lost a mixed tag team match.
On the May 6 episode, Long scheduled a World Heavyweight Championship match between Randy Orton and Christian who had just won it for the first time five nights previous at Extreme Rules. On the June 3 episode, Christian was chosen by Long as the special guest referee for a World Heavyweight Championship match between Orton and Sheamus who beat Christian and Mark Henry in a triple threat number one contender's match for the title the week before. Christian would turn heel by hitting Orton with the title he had retained and lost to Orton again at Capitol Punishment despite his foot being under the bottom rope. Christian blamed Long and as a result Long scheduled Orton to defend his title against Christian at Money in the Bank. Christian would manage to find a way to include a clause that if Orton were to get disqualified, the title would switch hands.
On the November 25, 2011 episode of SmackDown!, after Daniel Bryan seemingly successfully cashed in the Money In The Bank briefcase on The Big Show to win his first World Heavyweight Championship, Long rushed down to the ring and declared the title change void, as Mark Henry had not yet been medically cleared to compete in an official match. He would schedule Bryan in a fatal four-way match against Randy Orton, Cody Rhodes and Wade Barrett to determine the number one contender for Henry's world title which would be defended on the November 29 episode inside a steel cage.
After TLC: Tables, Ladders, and Chairs, Santino Marrella replaced Zack Ryder (who had just won his first United States Championship) for Smackdown Assistant General Manager.
On February 21, 2012, Long was criticized by Interim Raw General Manager John Laurinaitis, which resulted the WWE Board of Directors to switch the general managers of their respective shows for one week. Long took charge of the March 5 episode of Raw, with Laurinaitis taking charge of the March 9 edition of SmackDown. During Laurinaitis' time in charge of SmackDown, he set up a match between himself and Long, where, if Long won, Aksana, Long's girlfriend, would be placed in a match with Kane. Long won the match when Randy Orton attacked Kane at ringside, which distracted Laurinaitis.
A 12-man Tag match was then set up at WrestleMania XXVIII, where six superstars would represent both general managers. Long chose Santino Marella as his team captain, along with Kofi Kingston, R-Truth, Zack Ryder, The Great Khali and Booker T over the following weeks. A stipulation was added that the winning team at WrestleMania would determine who would become the general manager of both shows. At WrestleMania, Team Teddy lost to Team Johnny, ending Long's run as SmackDown General Manager.
On the April 6 edition of SmackDown, Long prepared to give his farewell speech, but Laurinaitis threatened to discontinue a trust fund Long had set up for his grandchildren's college education unless he took a job as his new assistant, to which Long reluctantly accepted.
For the next few weeks, Laurinaitis would humiliate Long by doing ridiculous antics; such as wearing a huge name tag and standing guard by his door as a Queen's soldier. When things would be go wrong, he would always blame Theodore saying, "Why Teddy?", in which the other heel wrestlers would agree.
On the 18th of June 2012 episode of Monday Night Raw, John Laurinaitis made a 3 on 1 handicap match featuring John Cena verses the trio of Big Show, David Otunga and John Laurinaitis. Big Show and David Otunga both left John Laurinaitis in the match making it 1 on 1. Teddy Long sat at ringside enjoying the final time that John Laurinaitis would be in a WWE ring as Laurinaitis got fired by Mr. McMahon at No Way Out 2012. He told John Cena to continue executing his finishing move on John Laurinaitis as Teddy Long looked on smiling. As Raw Supershow went off the air Teddy Long got up from his chair and attacked former General Manager John Laurinaitis. On June 29 episode of SmackDown!, Theodore Long announced that he would be the General Manager for both Smackdown and Raw that next week, then Long announced that Aksana and Cesaro would teamed up next Tuesday night against The Great Khali and the Divas Champion Layla in a mixed tag team match. On the August 3rd edition of Friday Night Smackdown, Theodore Long became the Senior Adviser to the General Manager of SmackDown, Booker T. Despite originally getting along with Booker very well, beginning in March 2013, Booker began to get angry at Teddy for booking matches without his permission on both Raw and SmackDown. However from mid April onwards, Teddy began running SmackDown again temporarily with Booker T away due to surgery. On the July 19th episode of Smackdown Vickie Guerrero was named Smackdown's new general manager and escorted Theodore Long out of the building.
On June 12, 2014, after nearly a year of inactivity, Long was released from WWE along with ten other contracts, ending his long tenure with the company. At the October 7th taping for the 15th Anniversray of Smackdown, Long made a suprise return; getting into an argument with John Laurinaitis. This lead to a 15 man Tag Team match, in which Team Teddy (Mark Henry, Sheamus, The Usos, Los Matadores, Jack Swagger and El Torito) defeated Team Johnny (Bo Dallas, Damien Mizdow/Sandow, Goldust, Stardust, Heath Slater, Titus O'Neil, Cesaro and Hornswoggle).
On the June 6, 2016 episode of Raw, Long returned in the opening segment between the Money in the Bank participants, requesting another run as General Manager of 'WWE SmackDown', only to be turned away by Stephanie McMahon. He would make several other appearances throughout the course of the night including his attempt of making a tag team match between The Golden Truth and Breezango before being escorted out of the building by security.