Franco, who is facing multiple allegations of sexual misconduct, sat for an Annie Leibovitz photo shoot and gave an interview for the magazine's annual Hollywood Portfolio, according to The Hollywood Reporter.
But after the allegations against "The Disaster Artist" surfaced, he was digitally removed from the cover.
"We made a decision not to include James Franco on the Hollywood cover once we learned of the misconduct allegations against him," a Vanity Fair spokesperson confirmed to The Hollywood Reporter.
The cover features actors Harrison Ford, Claire Foy, Nicole Kidman, Reese Witherspoon, Tom Hanks, Michael B Jordan, Zendaya, Jessica Chastain and others.
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He also received the Critics' Choice Award for his role but gave the ceremony a miss. Franco, however, attended the SAG Awards, which marked his first public appearance since the allegations surfaced.
Franco was accused online and in a Los Angeles Times report, after he showed up wearing the 'Time's Up' pin, like many other Hollywood stars, at the Globes
The 'Time's Up' campaign was launched by women in Hollywood to fight against sexual harassment in the wake of Harvey Weinstein expose.