Gellar attempted to capitalize on her television fame with a motion picture career, and had intermittent commercial success. After roles in the popular thrillers I Know What You Did Last Summer and Scream 2 (both 1997), she starred in the 1999 films Simply Irresistible, a romantic comedy, and Cruel Intentions, a modern-day retelling of Les Liaisons dangereuses. Cruel Intentions - with a kiss between Gellar and co-star Selma Blair that won the two the "Best Kiss" award at the 2000 MTV Movie Awards - was a modest hit at the box office, grossing over $38 million in the United States. Critic Roger Ebert stated that Gellar and co-star Ryan Phillippe "develop a convincing emotional charge" and that Gellar is "effective as a bright girl who knows exactly how to use her act as a tramp". Gellar’s role showed her versatility as an actress, and many were surprised to see her playing a brunette cocaine addict with an appetite for manipulating and using people. Her performance was praised by a number of critics, including Rob Blackwelder for SPLICEDwire, who wrote about the “dazzling performance by Sarah Michelle Gellar who plunges headlong into the lascivious malevolence that makes Kathryn so delightfully wicked. (Plus she looks great in a corset.)”.

Gellar next played a lead role in James Toback's critically unsuccessful independent Harvard Man (2001), where she played the daughter of a mobster. The movie included two strong sex scenes with Gellar, helping her shed her good girl image even more after Cruel Intentions in 1999. Rolling Stone said, "Yes, that's our Buffy, Sarah Michelle Gellar, playing a cheerleader who is not above sneaking off to the woods with her boyfriend, hiking up her skirt, sitting on his dick and bumping and grinding without missing a beat in the conversation. Gellar is a long way here from Scooby-Doo – thank the gods – and James Toback's Harvard Man is an even longer way from the Hollywood drool that pretends to take on issues – sexual, ethical, criminal – that often come with a college education". Sarah also starred as Daphne Blake in Scooby-Doo (2002), a live-action adaptation of the cartoon series. Gellar also appeared in the sequel, Scooby-Doo 2: Monsters Unleashed (2004). She starred alongside her husband, Freddie Prinze, Jr. in both Scooby-Doo movies. Gellar's next film was the 2004 horror film The Grudge, which was a success at the box office. David Wirtschafter, the president of the William Morris Agency (which represented Gellar), subsequently told The New Yorker that the success of The Grudge "takes our client Sarah Michelle Gellar, who now is nothing at all, and...makes her a star, potentially. Suddenly, the Sarah Michelle Gellar space is meaningful". The remark led Gellar to terminate her association with the agency; Gellar is now represented by the United Talent Agency.

Gellar appeared in the sequel The Grudge 2, which opened in October 2006; in the film, she has a minor role reprising her character from the first film. Gellar next appeared in the thriller The Return, which was released the following month. Sarah played a businesswoman haunted by memories of her childhood and the mysterious death of a young woman. The movie was marketed as a horror movie and many including critics were surprised to find The Return was as Rafe Telsch said "is just a murder mystery with a few supernatural elements". The movie pulled in a disappointing $4,800,000 weekend gross with little promotion. She then lent her voice to two animated films: the animated fairy tale Happily N'Ever After, and Teenage Mutant Ninja Turtles. She followed those with a string of films including Southland Tales, The Air I Breathe, Suburban Girl (earlier known as "A Girl's Guide to Hunting and Fishing"), and Possession (a supernatural thriller based on the South Korean film Jungdok known to English language audiences as Addicted). Southland Tales opened at the Cannes Film Festival in May 2006 and was released in the US in November 2007. The Air I Breathe and Suburban Girl were screened at the 2007 Tribeca Film Festival.

Suburban Girl eventually went straight to video in early 2008, much to fans' disappointment. It was dubbed a blend of Sex and the City and The Devil Wears Prada by the masses and a "pseudo-sophisticated romantic comedy" according to Variety.com Her on screen chemistry with Alec Baldwin was either criticised or praised, with Eye For Film commenting, "The film works best when Baldwin and Gellar are together - aside from the fact that Gellar seriously needs to eat a bun or two". Film website moviepictirefilm.com stated "Gellar and Baldwin both give wonderful performances and make their chemistry incredibly real and ultimately, quite heartbreaking. Containing a ton of laughs and killer fashion that could give "The Devil Wears Prada" a run for its money, this movie has something uncommon in most romantic comedies, tons of style and a huge heart." The Air I Breathe was released theatrically the same month to generally poor reviews. The New York Times called it a "gangster movie with delusions of grandeur." However, Gellar's performance was praised by a number of critics, DVD Talk Review noted that "her character here has the deepest emotional arc, and she hits all the right notes." She was offered a role in Stardust but turned it down to spend more time with her husband. Other roles she turned down include the role of Juliet in Romeo + Juliet (having had to turn it down due to scheduling conflicts with All My Children) and an undisclosed role in The Faculty. She was also offered the role of Brittany Foster in The In Crowd, but turned it down. The part later went to Susan Ward.

• This Side of the Looking Glass (2010) (pre-production) (rumored)
• The Wonderful Maladys (2009) (TV) (pre-production) (rumored)
• Veronika Decides to Die (2009) (completed) .... Veronika
  
• "Robot Chicken" .... Becky / ... (6 episodes, 2005-2009)
       - Love, Maurice (2009) TV episode (voice) .... Sarah Connor
       - Celebutard Mountain (2007) TV episode (voice) .... Blair Warner / Becky / Big Bad Wolf's Wife
       - 1987 (2006) TV episode (voice) .... Surgeon/Woman
       - Operation Rich in Spirit (2005) TV episode (voice) .... Daphne Blake / Samara Morgan
       - Joint Point (2005) TV episode (voice) .... Romance Woman/Various
        (1 more)
• Possession (2009) .... Jessica
• Suburban Girl (2007) .... Brett Eisenberg
• TMNT (2007) (voice) .... April O'Neil
  ... aka Teenage Mutant Ninja Turtles (USA: long title)
• The Air I Breathe (2007) .... Sorrow
  ... aka Fragmentos del destino (Mexico)
• Happily N'Ever After (2006) (voice) .... Ella
  ... aka Es war k'einmal im Märchenland (Germany)
• The Return (2006/I) .... Joanna Mills
• The Grudge 2 (2006) .... Karen
• Southland Tales (2006) .... Krysta Kapowski / Krysta Now
  ... aka Southland Tales (Germany: DVD title)
• The Grudge (2004) .... Karen Davis
  ... aka Der Fluch (Germany)
  ... aka The Juon (Japan)
• "The Simpsons" .... Gina (1 episode, 2004)
       - The Wandering Juvie (2004) TV episode (voice) .... Gina
• Scooby Doo 2: Monsters Unleashed (2004) .... Daphne
  ... aka Scooby-Doo 2: Monstres en liberté (Canada: French title)
• "God, the Devil and Bob" .... That Actress on That Show (1 episode, 2003)
       - There's Too Much Sex on TV (2003) TV episode (voice) .... That Actress on That Show
• "Buffy the Vampire Slayer" .... Buffy Summers / ... (145 episodes, 1997-2003)
  ... aka BtVS (USA: promotional abbreviation)
  ... aka Buffy (USA: short title)
  ... aka Buffy, the Vampire Slayer: The Series (USA: long title)
       - Chosen (2003) TV episode .... Buffy Summers
       - End of Days (2003) TV episode .... Buffy Summers
       - Touched (2003) TV episode .... Buffy Summers
       - Empty Places (2003) TV episode .... Buffy Summers
       - Dirty Girls (2003) TV episode .... Buffy Summers
        (140 more)
• Scooby-Doo (2002) .... Daphne Blake
• Jack Black: Spider-Man (2002) (TV) .... Mary Jane Watson / Wonder woman
• Lord of the Piercing (2002) (TV) .... Arwen
• Harvard Man (2001) .... Cindy Bandolini
• "Sex and the City" .... Debbie (1 episode, 2000)
       - Escape from New York (2000) TV episode .... Debbie
• "Angel" .... Buffy Summers (3 episodes, 1999-2000)
  ... aka Angel: The Series (USA: long title)
       - Sanctuary (2000) TV episode .... Buffy Summers
       - I Will Remember You (1999) TV episode .... Buffy Summers
       - The Bachelor Party (1999) TV episode (uncredited) .... Buffy Summers
  
• Cruel Intentions (1999) .... Kathryn Merteuil