Goldust came to the World Wrestling Federation on January 20, 2002, taking part in the Royal Rumble and reprising his Goldust character. He then feuded with Rob Van Dam before moving on to the hardcore division, where he won the Hardcore Championship on nine occasions.
When the World Wrestling Federation was renamed World Wrestling Entertainment and the roster was divided into two brands, Raw and SmackDown!, Goldust was assigned to the Raw brand, where he formed a tag team with Booker T. The duo engaged in numerous comedic vignettes, on one occasion hosting a segment titled Booker T and Goldust at the Movies and delivering reviews of The Scorpion King, a film starring The Rock. In May 2002, Booker joined the nWo, with Goldust's request to join the faction rejected. In June 2002, Booker was ejected from the nWo by Shawn Michaels, sparking a feud between the nWo and Booker and Goldust. Booker and Goldust went on to compete in the tag team division, winning the World Tag Team Championship at Armageddon before amicably splitting in January 2003.
Following the dissolution of the tag team, Rhodes developed a gimmick whereupon he contracted a stutter, as well as Tourette's-like symptoms (which continue to this day), upon receiving a shock from a junction box during an attack at the hands of Batista and Randy Orton. Rhodes appeared sporadically thereafter, forming a tag team with Lance Storm in August 2003, and was released in December 2003 following a period of inactivity.
Rhodes returned to World Wrestling Entertainment on October 31, 2005 as Goldust, as Jonathan Coachman enlisted him and Vader to attack Batista. Goldust and Vader unsuccessfully interfered in a Street Fight between Batista and Coachman on behalf of Coachman at Taboo Tuesday 2005. Following the event, Goldust once again disappeared from television.
In January 2006, Goldust took part in the Royal Rumble and was assigned once again to the Raw brand until he was released from his WWE contract on June 14, 2006 for no-showing an appearance.
On October 26, 2008, Rhodes appeared on WWE's Cyber Sunday under his Goldust persona as part of the three choices (the other two being Roddy Piper and The Honky Tonk Man) that the fans could choose to face Santino Marella for the Intercontinental Championship. After Honky Tonk Man was chosen and won via disqualification, Goldust and Piper entered the ring and the three candidates fought Marella, afterwards celebrating together in the ring. The following night on Raw, Goldust appeared again with Piper and the Honky Tonk Man as guest commentators for Marella's match with Charlie Haas. The match ended when Goldust and Piper distracted Marella so that Honky Tonk Man could smash his guitar over Marella's head.
Goldust appeared on the celebration of the 800th episode of Raw on November 3, 2008, dancing alongside his father Dusty Rhodes, Lilian Garcia and several other wrestlers, and finally made a full time return on the Raw roster once again on the November 24, 2008 edition of Raw, where he defeated Santino Marella, whom he would go on to defeat on multiple occasions. Goldust participated in the 2009 Royal Rumble match, but was eliminated by his real-life half-brother, Cody Rhodes. Goldust participated at WrestleMania XXV as a lumberjack during the tag team championship unification match between The Colóns and John Morrison and The Miz.
On May 25, episode of Raw, Goldust teamed up with Hornswoggle in a tag team match, where they defeated Festus and The Brian Kendrick. Goldust then teamed with Hornswoggle on multiple occasions, mainly feuding with Kendrick, where they had many matches both on WWE Superstars and Raw.
The team of Goldust and Hornswoggle came to an end on June 29, 2009 when Goldust was traded to the ECW brand via a 15-man trade, marking the first time that Rhodes has been on another brand other than Raw. His debut match for the brand came on the July 14 episode of ECW, in which he lost to Zack Ryder. In the upcoming weeks, he started a feud with Sheamus leading to his first televised singles win in several months on WWE Superstars against Sheamus. Ultimately, he lost the feud in a "No Disqualifications" match on the September 1st episode of ECW on SyFy.
Following this loss, he garnered his first number one contender's match for the ECW World Championship on the September 15, 2009 edition of ECW on SyFy in a 10-Man Battle Royal where he was the seventh participant eliminated and Zack Ryder earning the title shot in the end. The September 29, 2009 edition of ECW on SyFy saw Goldust win his first match on ECW in an 8-Man Tag-Team match where Yoshi Tatsu pinned William Regal to score the win for their team. Goldust debuted a new finishing maneuver called the "Golden Age" on the October 22, 2009, edition of WWE Superstars, when he and Tommy Dreamer defeated Vladimir Kozlov and Ezekiel Jackson..