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With Rushmore, Wes Anderson and Owen Wilson wanted to create their own "slightly heightened reality, like a Roald Dahl children's book". Like Max Fischer, Wilson was expelled from his prep school, St. Mark's School of Texas, in the tenth grade, while Anderson shared Max's ambition and lack of academic motivation, and also had a crush on an older woman. Anderson and Wilson began writing the screenplay for Rushmore years before they made Bottle Rocket. They knew that they wanted to make a film set in an elite prep school, much like St. Mark's, which Owen had attended along with his two brothers, Andrew and Luke (Luke being the sole graduate), and St. John's School in Houston, Texas which Anderson had attended.
The film also featured M. B. Lamar High School. According to the director, "One of the things that was most appealing to us was the initial idea of a 15-year-old kid and a 50-year-old man becoming friends and equals". Rushmore was originally going to be made for New Line Cinema but when they could not agree on a budget, Anderson, Wilson and producer Barry Mendel held an auction for the film rights in mid-1997 and struck a deal with Joe Roth, then-chair of Walt Disney Studios. He offered them a $10 million budget. The film was distributed by Touchstone Pictures, and produced by Barry Mendel and Paul Schiff for American Empirical Pictures.
Anderson and Wilson wrote the role of Mr. Blume with Bill Murray in mind but doubted they could get the script to him. Murray's agent was a fan of Anderson's first film, Bottle Rocket, and urged the actor to read the script for Rushmore. Murray liked it so much that he agreed to work for scale, which Anderson estimated to be around $9,000. The actor was drawn to Anderson and Wilson's "precise" writing and felt that a lot of the film was about "the struggle to retain civility and kindness in the face of extraordinary pain. And I've felt a lot of that in my life". Anderson created detailed storyboards for each scene but was open to Murray's knack for improvisation.
Casting directors considered 1,800 teenagers from the United States, Canada, and Britain for the role of Max Fischer before finding Jason Schwartzman. In October 1997, approximately a month before principal photography was to begin, a casting director for the film met the 17-year-old actor at a party thanks to Schwartzman's cousin, filmmaker Sofia Coppola. He came to his audition wearing a prep-school blazer and a Rushmore patch he had made himself. Anderson almost did not make the film when he could not find an actor to play Max but felt that Schwartzman "could retain audience loyalty despite doing all the crummy things Max had to do". Anderson originally pictured Max, physically, as Mick Jagger at age 15, to be played by an actor like Noah Taylor in the Australian film Flirting - "a pale, skinny kid". When Anderson met Schwartzman, he reminded Anderson much more of Dustin Hoffman and decided to go that way with the character. Anderson and the actor spent weeks together talking about the character, working on hand gestures and body language.
Anderson confirmed that the protagonist Max is a semi-autobiographical version of himself, including his tendency to write school plays, except that Max is not shy.
Wes Anderson originally intended for the film's soundtrack to be entirely made up of songs by The Kinks, feeling the music suited Max's loud and angry nature, and because Max was initially envisioned to be a British exchange student. However, while Anderson listened to a compilation of other British Invasion songs on the set, the soundtrack gradually evolved until only one song by the Kinks remained in the film ("Nothin' in the World Can Stop Me Worryin' 'Bout That Girl").
Bill Murray genuinely found Keith McCawley and Ronnie McCawley, who play his sons, annoying (much like their screen characters), and many of the scenes where he lashes out at them and insults them were improvised.
According to Bill Murray, he disliked Jason Schwartzman's personality during their first meeting. But he eventually warmed up to him while they worked together.
Before the film's theatrical release, co-writer and director Wes Anderson arranged a private screening for one of his adolescent heroes, the critic Pauline Kael. The film thoroughly mystified Kael, who at that stage was retired, nearly 80, and being treated for Parkinson's disease.