Flinn was also a writer. His first work was What They Did for Love: The Untold Story Behind the Making of A Chorus Line (1989), covering the story behind the production of the 1970s musical A Chorus Line. He next turned to mystery fiction, writing the novels San Francisco Kills (1990) and Killer Finish (1991). His only other novel was The Fearful Summons (1995), a Star Trek novel. His research work Musical! A Grand Tour - the Rise, Glory and Fall of an American Institution (1997) won an ASCAP Deems Taylor Award. His later output consisted of non-fiction books such as How Not To Write a Screenplay: 101 Common Mistakes Most Screenwriters Make (1999) and How Not To Audition: Avoiding the Common Mistakes Most Actors Make (2003).