He has also appeared in Anderson's The Life Aquatic with Steve Zissou (2004), The Darjeeling Limited (2007), Fantastic Mr. Fox (2009), The Grand Budapest Hotel (2014), and The French Dispatch (2021).

Wilson also starred in the Woody Allen romantic comedy Midnight in Paris (2011) as disenchanted screenwriter Gil Pender, a role which received a Golden Globe Award nomination.

His voice acting roles include Lightning McQueen in the Cars film series (2006–2017), the titular character in Marmaduke (2010), and Reggie in Free Birds (2013).

[9] That same year, he had a supporting role in the black comedy The Cable Guy (1996) starring Jim Carrey and directed by Ben Stiller, an early admirer of Bottle Rocket.

[10][11][12] After appearing in supporting roles in 1999, he acted in horror film The Haunting, The Minus Man, in which his future girlfriend, singer Sheryl Crow, was a co-star.

Gene Hackman reportedly took notice of Wilson's performance in Shanghai Noon and recommended the actor to co-star in the 2001 action film Behind Enemy Lines.

He then reunited with Chan to make Shanghai Knights (2003), and co-starred in the film remake of the 1970s television series Starsky & Hutch (2004).

Due to his busy schedule as an actor and an ongoing sinus condition, Wilson was unavailable to collaborate on the script for Wes Anderson's fourth feature film, The Life Aquatic with Steve Zissou.

However, Wilson did star in the film as Bill Murray's would-be son, Ned Plimpton; it was a role written specifically for him.

[16] In 2006, Wilson voiced Lightning McQueen in the Disney/Pixar film Cars, starred in You, Me and Dupree with Kate Hudson, and appeared with Stiller in Night at the Museum as cowboy Jedediah.

He appeared in a film adaptation of John Grogan's best-selling memoir, Marley & Me (2008), co-starring Jennifer Aniston.

[20] He provided the voice for the Whackbat Coach Skip in Wes Anderson's stop motion animated film Fantastic Mr. Fox (2009).

Wilson made a guest appearance on the NBC comedy Community with fellow Frat Pack member Jack Black.

[21] In 2011, Wilson starred as a nostalgia-seized writer in the romantic comedy Midnight in Paris, written and directed by Woody Allen.

[25] For his performance, Wilson earned a nomination for the Golden Globe Award for Best Actor – Motion Picture Musical or Comedy.

[26] The film was released in October 2011 by 20th Century Fox, and co-starred Jack Black, JoBeth Williams, Steve Martin and Rashida Jones.

In March 2012, Wilson was signed to star in the John Erick Dowdle thriller The Coup,[27] later renamed "No Escape", in which he played the role of the father of an American family that moves to Southeast Asia, only to find itself swept up in a wave of rebel violence that is overwhelming the city.

[34] In 2021, Wilson starred in the comedy film Bliss, directed by Mike Cahill opposite Salma Hayek for Amazon Studios.