For his work in film, Flaherty was nominated for two Academy Awards with lyricist Ahrens (for Best Song and Best Score, the latter shared with David Newman) and two Golden Globe Awards for his first film, Twentieth Century Fox's animated "Anastasia" (1997). He also composed the film score and wrote the songs for its animated sequel, "Bartok The Magnificent" (1999). He wrote the original film score for the documentary "After the Storm" (2009), which follows a group of teenagers as they perform Ahrens and Flaherty's "Once On This Island" in New Orleans post-Hurricane Katrina. He composed the song score and co-wrote the film score for "Lucky Stiff" (2014), which was based on his and Ms. Ahrens’ stage musical of the same name.