Native Son is mentioned in a flashback in the film American History X (1998), when Derek's father criticizes Derek's teacher for including lessons on African-American literature and affirmative action.
An allusion to the story is presented in part 1 of The Second Renaissance (2003), a short anime film from The Animatrix collection. In this film, a domestic robot named "B1-66ER" is placed on trial for murder. The name is created using Leet Speak.
In the motion picture The Help (2011), the main character (played by Emma Stone) is seen in an oblique camera angle to have a copy of Native Son on her bookshelf.
In Cecil Brown's novel The Life and Loves of Mr. Jiveass Nigger (1969), the protagonist, George Washington, states that he is not fearful, that he is not a "Bigger Thomas".
Native Son is mentioned in Edward Bunker's novel Little Boy Blue (1981) as being read while in solitary confinement by the main character, Alex Hammond, who is said to be greatly fascinated by it.
A large section of Percival Everett's Erasure (1999) contains a parody of Native Son, entitled "Fuck".
A line from the trial speech by Bigger Thomas' lawyer, Boris Max, is woven into the plot of The Penultimate Peril (2005), a book by Lemony Snicket. "Richard Wright, an American novelist of the realist school, asks a famous unfathomable question.... 'Who knows when some slight shock,' he asks, 'disturbing the delicate balance between social order and thirsty aspiration, shall send the skyscrapers in our cities toppling?' .. So when Mr. Wright asks his question, he might be wondering if a small event, such as a stone dropping into a pond, can cause ripples in the system of the world, and tremble the things that people want, until all this rippling and trembling brings down something enormous,..."
In Ron Suskind's 1998 book, A Hope in the Unseen, Native Son is referenced during a discussion the main character takes part in at Brown University.
Bigger Thomas is mentioned in one of the lyrical hooks of "The Ritual" in Saul Williams' The Inevitable Rise and Liberation of NiggyTardust! (2007).
The U2 song "Vertigo" was called "Native Son" by the band during the recording sessions for How to Dismantle an Atomic Bomb (2004). The song was later released in the collections Unreleased & Rare (2004) and U2: Medium, Rare & Remastered (2009).
On the HBO series Brave New Voices, during the 2008 finals, the Chicago team performed a poem called "Lost Count: A Love Story". This poem addresses the youth on youth murder in Chicago and includes the phrase: "Being brown in Bigger Thomas' town".
In the Star Trek: Deep Space Nine episode, "Far Beyond the Stars" (1998), Benny Russell cites Native Son as an example of a significant work of African-American literature.