According to The Hollywood Reporter, the actor, 39, sat for the Annie Leibovitz photoshoot and was interviewed for the special edition.
But it says Franco was removed digitally before publication, quoting a magazine spokesman as saying: “We made a decision not to include James Franco on the Hollywood cover once we learned of the misconduct allegations against him.”
The Disaster Artist actor was accused of sexual misconduct, in a report in the Los Angeles Times, by five women.
He has denied allegations against him, calling them “not accurate”.
The Crown star Claire Foy appears alongside a host of big screen heavyweights including Nicole Kidman, Oprah Winfrey, Reese Witherspoon, Tom Hanks, Robert De Niro and Harrison Ford on the US magazine’s annual fold-out cover.
Michael B Jordan, Zendaya, Jessica Chastain, Michael Shannon, Gal Gadot and Vanity Fair’s outgoing editor Graydon Carter complete the line-up.
Vanity Fair said it picked this year’s cover stars based on their influence at a time when the #MeToo movement is in full swing.
Allegations against Franco surfaced in the wake of his Golden Globe win for The Disaster Artist.
He was later snubbed for an Oscar nomination, missing out on a best actor nod for his portrayal of The Room’s eccentric filmmaker Tommy Wiseau.