She was born in Kansas City, Missouri and raised in midtown Kansas City's Coleman Highlands neighborhood. Both of her parents were professors at Metropolitan Community College–Penn Valley: her mother, Judith Ann (née Schieber), was a reading-comprehension professor, and her father, Edwin Matthew Flynn, was a film professor. She has an older brother, Travis, who is a railroad machinist. Her uncle is Jackson County Circuit Court Judge Robert Schieber. Flynn was "painfully shy" and found escape in reading and writing. Growing up, Flynn's father would take her to watch horror movies.

After attending Bishop Miege High School and graduating in 1989, she attended the University of Kansas, where she received her undergraduate degrees in English and journalism. She spent two years in California writing for a trade magazine for human resources professionals before moving to Chicago and attending Northwestern University for a Master's degree at its Medill School of Journalism in 1997. Flynn initially wanted to work as a police reporter, but chose to focus on her own writing as she discovered she had "no aptitude" for police reporting.
After graduating from Northwestern, Flynn worked freelance briefly at U.S. News & World Report before being hired as a feature writer in 1998 at Entertainment Weekly. She was promoted to television critic and wrote about films, but was laid off in December 2008.
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