I do not think there is a single theme of the novel Prep. I think there are several themes portrayed throughout the novel. One theme that I see is the theme of wealth and social class. Because Lee Fiora won a scholarship to attend the Ault school, she is not there because her family can afford to send her there. Not only does she feel like an outsider, but she is treated like one because she doesn't do things like summer on Nantucket. The book's examination of wealth and social class really shows how those two things can open and close a lot of doors for teens.
I see a theme of loneliness. Lee is a lonely character. She doesn't have any close friends, save maybe her roommate. She is extremely isolated in a world that doesn't fit with her. It's phony. It's not surprising that literary critics have compared Lee and the novel to Holden Caufield and The Catcher in the Rye.
Love and sexuality are two themes present in the book as well. Lee develops a crush of sorts on a boy, and the book also has the stereotypical ostracized gay student.