The tennis star features on one of four covers for the December issue of the US men’s magazine, alongside actors Michael B Jordan, Henry Golding and Jonah Hill.
On hers, the word men is crossed out and replaced by the word “woman” – in a different font and in quotation marks.
It has drawn criticism on social media, with many Twitter users questioning the use of the punctuation.
One Twitter user said: “Someone didn’t think that through very well. I doubt there were bad intentions but people will put a negative spin on anything they can.”
At the bottom of the page, it says the handwriting is by designer Virgil Abloh, who has designed Nike outfits for Williams – and includes quotation marks in his work.
Responding to one Twitter user, Mick Rouse, a GQ research manager, according to his Twitter bio, explained:
“100% understand the concerns your raising, and it’s not something lost on me. But that’s the truth behind the cover,” Mr Rouse tweeted later on.
It comes after a difficult time for Williams, who returned to work after she “almost died” following the birth of her daughter Olympia in 2017, and then struggled with postnatal depression.
She made it to the Wimbledon final in a remarkable comeback, but later made headlines after being given three warnings for coaching, smashing her racket and calling the umpire a thief in a tense US Open final in September.
A cartoon mocking her behaviour appeared in an Australian newspaper, sparking allegations of racism for its depiction of an angry Williams jumping on a broken tennis racket.
Sky News has contacted GQ and agents for Williams for comment on the GQ cover.