Dykstra made his first appearance in WWE on the May 12, 2003 episode of WWE Raw as Ken Phoenix. Along with his brother, Mike Phoenix, he was a participant in Rodney Mack's ongoing "5-Minute White Boy Challenge", where Mack defeated Caucasian wrestlers in under five minutes. Mack defeated the pair in 1:31, forcing them both to submit to his new Blackout finishing hold. He made another appearance, losing to Lance Storm on an episode of Sunday Night Heat.
In early 2006, Dykstra became a part of the Spirit Squad, a faction using the in-ring personas of male cheerleaders, using the name "Kenny". On the January 23, 2006, episode of Raw, the group helped Jonathan Coachman win a Royal Rumble qualifying match against Jerry "The King" Lawler by performing cheers for Coachman and distracting Lawler. They later became a part of the ongoing feud between WWE chairman Vince McMahon and Shawn Michaels. The villainous McMahon brought in the Squad to attack Michaels on numerous occasions, including placing them in multiple handicap matches.
They also continued wrestling in the tag team division, and on April 3, on Raw, the Squad won the World Tag Team Championship when Kenny and Mikey, with outside help from the other three Squad members, defeated the team of Big Show and Kane. After winning the championship, all five members of the team were recognized as the champions, allowing any combination of them to defend the championship.
Three weeks later, McMahon scheduled another handicap match, with the Spirit Squad facing Michaels. The match never started, however; instead the Spirit Squad brutally beat down Michaels, ripping apart his ring attire and, as part of the storyline, shattered his knee with a chair. McMahon then called Triple H to the ring to attack Michaels with a sledgehammer; however, Kenny snatched the sledgehammer away from him, disrespecting Triple H, which led to him attacking the group. Triple H and Michaels revived their former team, D-Generation X (DX), and began a feud with the Spirit Squad. DX played various sophomoric pranks on the team and the McMahons (Vince and his son Shane), as well as defeating the Spirit Squad in handicap tag team matches at Vengeance and a clean sweep in an elimination handicap match at Saturday Night's Main Event XXXIII.
At the same time as their feud with DX and their alignment with McMahon, the team also wrestled other teams in Raw's tag division over the World Tag Team Championship. The group successfully defended the tag team championship against the teams of Jim Duggan and Eugene, Charlie Haas and Viscera, and Snitsky and Val Venis. They then entered a lengthy feud with The Highlanders, whom they eventually defeated to retain the titles at Unforgiven.
The Squad as a whole later began a losing streak with separate members losing singles matches to Ric Flair on consecutive episodes of Raw. After two consecutive losses to the debuting Cryme Tyme, Kenny attacked Mikey on the October 23 episode of Raw, and announced that he was going to defeat Flair. Kenny was successful, despite Flair attempting to even the odds by bringing other WWE Legends (Dusty Rhodes, Sgt. Slaughter, and "Rowdy" Roddy Piper) to the ring with him. It was then announced that Flair and a legend, selected by interactive voting, would wrestle the team for the World Tag Team Championship at the Cyber Sunday pay-per-view in early November. The fans chose Piper, and he and Flair defeated Kenny and Mikey to win the championship.
The group disbanded on the November 27 Raw after losing a five-on-three match against Flair and DX. Later that night, DX placed all five members into a crate.
After the breakup of the Spirit Squad, he was repackaged as Kenny Dykstra, with new attire and entrance music. He became interested in joining the group Rated-RKO, which consisted of Edge and Randy Orton. In order to join, he was told to prove himself first. He continued the feud with Ric Flair, managing to pick up three straight victories before finally losing to him on the January 15, 2007, episode of Raw. Dykstra competed in the 2007 Royal Rumble match and got eliminated by Edge. After his feud with Flair, Dykstra become a mainstay on Raw's sister show Heat, having feuds with both Eugene and Val Venis.
He then formed a tag team with Johnny Nitro, but the duo split when Kenny was drafted to the SmackDown! brand on June 17, 2007, as part of the WWE Supplemental Draft, while Nitro was drafted to ECW.
Dykstra made his debut on the July 6 episode of SmackDown! in a losing effort to the re-debuting Chuck Palumbo. On the July 20 episode of SmackDown!, Dykstra participated in a 20-man battle royal for the World Heavyweight Championship and was eliminated by Chris Masters; later on that evening, he lost to Matt Hardy in singles competition.
Dykstra formed an on-screen relationship with Victoria on the July 27 episode of SmackDown!. The two teamed together in mixed tag team matches, usually against Jimmy Wang Yang and Torrie Wilson or Chuck Palumbo and Michelle McCool. They also regularly accompanied each other to the ring for matches.
After a leave of absence from television in the first half of 2008, Dykstra made his return on the August 15 episode of SmackDown, losing to WWE Champion Triple H. On November 10, 2008, WWE announced Dykstra had been released from his contract.
In late 2016, Kenny and Mikey returned to WWE for a short storyline with Dolph Ziggler (formerly Nicky in the Spirit Squad). On October 4, on SmackDown, they utilised their Spirit Squad characters to taunt Ziggler about his time in the Spirit Squad, before attacking him at the behest of Intercontinental Champion The Miz and Maryse. Five days later, at the No Mercy pay-per-view, he and Mikey tried to distract Ziggler in his career versus title match under Maryse's command, but were unsuccessful in doing so. On the October 11 episode of SmackDown, Kenny and Mikey faced Ziggler in a two-on-one handicap match; Ziggler won but was then attacked by The Miz and saved by Rhyno and Heath Slater. This led to a six-man tag team match the following week, in which Kenny, Mikey, and The Miz won when Kenny pinned Slater. Kenny and Mikey unsuccessfully challenged Slater and Rhyno for the WWE SmackDown Tag Team Championship on October 25. They appeared throughout November in tag team matches, before disappearing off television.
In December 2021, Dykstra began working as a producer on Raw and SmackDown.