Two years after her departure from Charmed, Doherty hosted the Sci Fi Channel candid camera show Scare Tactics during its initial season. It is unsure why she left the show. Doherty's hosting position was given to Stephen Baldwin for the season two cycle; however, the series stopped production in 2006 after the second season's end. After a three and a half year hiatus, the series returned in July 2008 with host Tracy Morgan. After her stint on Scare Tactics Doherty, in a return to her prime-time soap roots, starred as a regular on the short-lived TV series North Shore. She starred as Alexandra Hudson from 2004–2005. Later in 2005, Doherty was cast in the new TV comedy Love Inc. Although she filmed the original pilot, she was dropped from the show just months before its debut.

Doherty later went on to produce and star in her own reality show, Breaking Up With Shannen Doherty, which premiered on the Oxygen network in 2006. In the show Doherty goes around doing "dirty work" for members of the public, including dumping boyfriends or telling people what their friends really think about them. The show was canceled after one season due to a small audience. She also starred in the popular British sitcom Bo! in the USA, a program of brain child Leigh Francis. In the show, she plays herself, being randomly harassed by Avid Merrion (Francis) who claims they are lovers. The show aired in October 2006 on the British channel 4, and she appeared in several episodes. In 2007, Doherty appeared in two television projects. First up was the pilot Kiss Me Deadly: A Jacob Keane Assignment for the here! network, and then the holiday picture Christmas Caper for ABC Family. That same year Doherty also set up a production company called "No Apologies" where she’s developing a TV-drama for herself. In 2007 Doherty was also ranked as number 96 on Entertainment Weekly's list of the 100 Greatest Television Icons.

In 2008, Doherty was featured on the Swedish television show High Chaparall, appearing in the second episode of the show’s fourth season. Later that year, it was confirmed that Doherty would join the cast of the Beverly Hills, 90210 spin off for the CW Television Network, for a reported $40,000–50,000 an episode. She returned as a guest star, reprising her old role of Brenda Walsh in four of the new series' initial six episodes. Her character, now a successful theater actress and stage director, returned as the guest director of the high school musical. After her initial guest spot was completed, Doherty stated she was open to returning to the series later in the season and eventually agreed to appear in three additional episodes with her most recent appearance slated to air in May 2009.

The writers were eager to have her share scenes with Jennie Garth who also reprised her 90210 role of Kelly Taylor. It was reported that Doherty and Garth's characters would both have a romantic interest in the character Ryan Matthews (Ryan Eggold), reminiscent of their old rivalry for former bad boy character Dylan McKay (Luke Perry). Doherty and Garth later confirmed that the reports about the love triangle between their characters were false. Doherty also has an upcoming role in the SciFi Channel’s adventure film, The Lost Treasure of the Grand Canyon as Susan Jordan opposite Michael Shanks and Bianca Owens. The film is currently in post-production and is set for a 2008/2009 premiere on the cable network. She is also in the process of pitching a new television show to networks. On October 30, 2008, TV Guide reported that Doherty is due to co-star alongside Dylan McDermott in the indie film Burning Palms, a satire based on Los Angeles stereotypes told through five intertwining storylines. She will also be starring in the upcoming TV movie thriller Resistance with Mark Humphrey.

• Resistance (2009) (TV) (filming) (rumored) .... Claire
• Burning Palms (2009) (post-production) .... Dr. Shelly
  
• "90210" .... Brenda Walsh (6 episodes, 2008-2009)
       - Hello, Goodbye, Amen (2009) TV episode .... Brenda Walsh
       - That Which We Destroy (2008) TV episode .... Brenda Walsh
       - Model Behavior (2008) TV episode .... Brenda Walsh
       - Wide Awake and Dreaming (2008) TV episode .... Brenda Walsh
       - The Bubble (2008) TV episode .... Brenda Walsh
        (1 more)
• The Lost Treasure of the Grand Canyon (2008) (TV) .... Susan Jordan
• Kiss Me Deadly (2008) (TV) .... Marta
• Christmas Caper (2007) (TV) .... Kate Dove
• Category 7: The End of the World (2005) (TV) .... Faith Clavell
• "Love, Inc." .... Denise Johnson (1 episode, 2005)
       - Pilot (2005) TV episode (uncredited) .... Denise Johnson
• "North Shore" .... Alexandra Hudson (11 episodes, 2004-2005)
       - The End (2005) TV episode .... Alexandra Hudson
       - The Ex-Games (2005) TV episode .... Alexandra Hudson
       - Shark (2005) TV episode .... Alexandra Hudson
       - Catwalk (2004) TV episode .... Alexandra Hudson
       - Sucker Punch (2004) TV episode .... Alexandra Hudson
        (6 more)
• Nightlight (2003) (TV) .... Celeste
  ... aka View of Terror (Canada: English title: cable TV title) (UK: DVD title) (USA)
  ... aka Une vue terrifiante (Canada: French title)
• Hell on Heels: The Battle of Mary Kay (2002) (TV) .... Lexi Wilcox
  ... aka Empire de Mary Kay, L' (Canada: French title)
  ... aka The Battle of Mary Kay (UK)
• The Rendering (2002) .... Sarah Reynolds
  ... aka Portrait macabre (Canada: French title)
  ... aka Portrait of a Murder (USA: TV title)
• Another Day (2001) (TV) .... Kate
  ... aka Passion impossible (Canada: French title)
• "Charmed" .... Prue Halliwell (67 episodes, 1998-2001)
       - All Hell Breaks Loose (2001) TV episode .... Prue Halliwell
       - Look Who's Barking (2001) TV episode .... Prue Halliwell
       - Exit Strategy (2001) TV episode .... Prue Halliwell
       - The Demon Who Came in from the Cold (2001) TV episode .... Prue Halliwell
       - Sin Francisco (2001) TV episode .... Prue Halliwell
        (62 more)
• Satan's School for Girls (2000) (TV) .... Beth Hammersmith/Karen Oxford