The 'Judas' singer, wearing a fuchsia Marc Jacob gown, was photographed by Mert & Marcus.
GaGa unveiled the cover on her new social network littlemonsters.com, posting: "SHH DONT TELL TWITTER/ SEPT ISSUE OF VOGUE MAGAZINE/ Sorry Anna but the underground kids deserve it. bisous!"
The message referred to Anna Wintour, the editor-in-chief of Vogue.
Vogue's September issue is a coveted issue in the fashion world and was the focus of a 2009 documentary, aptly titled The September Issue.
Speaking to Vogue about her music, Lady GaGa said: "I don't really make records for people to listen to and go, 'Wow, she's a genius'. I'd really like you to order a drink, maybe kiss the person you came with that evening or rediscover something about your past that makes you feel even more brave."
She also recounted a highlight of her 'Born This Way Ball' tour.
"We were talking about putting the show together and I said, 'Okay, what if I was someone's grandma and I was going to a concert tonight'," GaGa said. "How would I know that it was a GaGa show?
"We all just sort of looked at each other and said, 'The meat dress'."
The September issue of Vogue featuring Lady GaGa is available from next Tuesday (August 14).
Watch the music video for 'Judas' by Lady GaGa below: