Flynn grew up in Kansas City, Missouri. Both of her parents were teachers at a local community college. Her mother taught reading and her father taught film. Growing up surrounded by books and movies strongly shaped her imagination and later influenced her interest in storytelling and dark, character-driven fiction. 

After graduate school, Flynn worked as a journalist. She became a staff writer and later a television critic for the entertainment magazine Entertainment Weekly, where she wrote about film and TV. In 2008, during company cutbacks, her position was eliminated. Losing that job pushed her to focus on fiction writing full time.