In 2000, Perabo was cast in The Adventures of Rocky and Bullwinkle as lead character FBI agent Karen Sympathy. Her next film, Coyote Ugly was more of a star-making role. She played Violet Sanford, nicknamed "Jersey," a young woman who moves to New York to pursue her dream of becoming a songwriter. Perabo took lessons in voice, guitar, piano and bartending to prepare for the role. Despite poor reviews, the film was a modest box-office success and she won an MTV Movie Award for Best Music Moment for "One Way or Another."

In 2001, Perabo starred in an independent Canadian movie called Lost and Delirious, playing a boarding school student who falls in love with a female classmate. The next year she starred as a French exchange student in Slap Her... She's French, which was shelved in North America for two years, then released under the new title She Gets What She Wants. The film was released under its original title in Europe. In 2003, she had a role as the eldest Baker child, Nora, in Cheaper by the Dozen (2003) which she reprised in its 2005 sequel.

Other recent films include The i Inside (2003), Perfect Opposites (2004), George and the Dragon (2004), The Cave (2005), Imagine Me & You (2005), Edison (2005), and The Prestige (2006). She has also appeared as a nutritionist on the Fox TV show House. In 2008 Perabo played a lead role in the Neil LaBute theater play Reasons to Be Pretty.

• Sordid Things (2008) (completed) .... Tabitha White
• Ashes (2009) .... Bettina
• The Lazarus Project (2008) .... Lisa Garvey
• Beverly Hills Chihuahua (2008) .... Rachel Ashe Lynn
• The Prince of Motor City (2008) (TV)
• "House M.D." .... Honey (1 episode, 2007)
  ... aka House (South Africa: English title) (USA: short title)
       - Resignation (2007) TV episode .... Honey
• Carriers (2007) .... Bobby
• In Vivid Detail (2007) .... Leslie
• Because I Said So (2007) .... Mae
• The Prestige (2006) .... Julia McCullough / Angier
• First Snow (2006/I) .... Deirdre
• 10th & Wolf (2006) .... Brandy
• Cheaper by the Dozen 2 (2005) .... Nora Baker-McNulty
• Good Morning Baby (2005) .... Gabriella
• Edison (2005) .... Willow Summerfield
  ... aka Edison Force (USA: DVD title)
• Imagine Me & You (2005) .... Rachel
  ... aka Eine Hochzeit zu dritt (Germany)
  ... aka Imagine Me and You (Canada: English title: festival title)
• The Cave (2005) .... Charlie
• Karas: The Prophecy (2005) (V) (voice: English version) .... Yurine
• Perception (2005) .... Jen
• George and the Dragon (2004) .... Princess Luma
  ... aka Dragon Sword (USA: TV title)
  ... aka George und das Ei des Drachen (Germany)
• Perfect Opposites (2004) .... Julia Bishop
• Cheaper by the Dozen (2003) .... Nora Baker
• The I Inside (2003) .... Anna
• Flowers (2002/I) .... Iris
• Slap Her... She's French (2002) .... Genevieve Le Plouff
  ... aka Freche Biester! (Germany)
  ... aka She Gets What She Wants (USA: TV title)
• Lost and Delirious (2001) .... Pauline 'Paulie' Oster
  ... aka Rage au coeur, La (Canada: French title)
  ... aka Rebelles (Canada: French title)
• Followers (2000) .... Girl at Party
• Coyote Ugly (2000) .... Violet Sanford
• The Adventures of Rocky & Bullwinkle (2000) .... Karen Sympathy
  ... aka Die Abenteuer von Rocky und Bullwinkle (Germany)