Gone Girl's themes include dishonesty, the devious media, and the unhappiness that comes with a troubled economy. The characters lie to each other and the reader about affairs and disappearances. Amy makes a fake diary to implicate her husband for her disappearance and murder. Flynn says that, in writing the book, she wanted to examine how people within a marriage lie to each other: "marriage is sort of like a long con, because you put on display your very best self during courtship, yet at the same time the person you marry is supposed to love your warts and all. But your spouse never sees those warts really until you get deeper into the marriage and let yourself unwind a bit." Also certain aspects taken from Charlie and the Great Glass elevator.
An underlying theme is the brief undertone of feminism, most notably represented in Amy's infamous 'Cool Girl' speech. For some, it is in this monologue that the otherwise despised Amazing Amy emerges as an unlikely heroine of sorts; flying the flag for women who refuse to succumb to the pressure to morph into the male's ideal. Flynn is a self-identified feminist and has stated that Amy's "just pragmatically evil" character and non-conformity to the traditional perception of women as innately good characters are the embodiment of feminism, which she defined as "the ability to have women who are bad characters".
Several reviews have also noted how well Gone Girl shows the tricky nature of media representation. Nick seems guilty due to media coverage before a trial occurs. Salon.com notes that "Flynn, a former staff writer for Entertainment Weekly, is especially good on the infiltration of the media into every aspect of the missing-person investigation, from Nick's cop-show-based awareness that the husband is always the primary suspect to a raving tabloid-TV Fury who is out to avenge all wronged women and obviously patterned on Nancy Grace." Entertainment writer Jeff Giles notes that the novel also plays on reader expectations that the husband will be the murderer, expectations that have also been shaped by the media, writing, "The first half of Gone Girl is a nimble, caustic riff on our Nancy Grace culture and the way in which The butler did it has morphed into 'The husband did it.'". A New York Daily News review also notes the novel's interest in how quickly a husband can be convicted in the media: "In a media society informed by Nancy Grace, when a wife goes missing, the husband murdered her. There’s no need for a body to arrive at a verdict. A San Francisco Chronicle review also notes the book's recurring commentary on media influence: "Flynn pokes smart fun at cable news, our collective obsession with social media and reality TV."
Flynn has also said that she wanted this novel to capture the sense of bankruptcy that both individuals and communities feel when the economy spirals. Not only have both her main characters lost their jobs, they have also moved to a town that is blighted by unsold houses and failed businesses. "I wanted the whole thing to feel bankrupt ... I wanted it to really feel like a marriage that had been hollowed out in a city that had been hollowed out and a country that was increasingly hollowed out," said Flynn.