The "Girls" star praised the magazine for not digitally editing her cellulite, adding that she hopes the image will help with "normalising the female form".
"Whether you agree with my politics, like my show or connect to what I do, it doesn't matter - my body isn't fair game," she said on Instagram.
"No one's is, no matter their size, colour, gender identity, and there's a place for us all in popular culture to be recognised as beautiful."
Dunham appears on the cover with her "Girls" costars, known of whom have been digitally edited in the issue.
On Instagram Dunham said that throughout her teens, people made her aware that she didn't fit in with society's beauty standards.
"I was told, in no uncertain terms, that I was fucking funny looking," she said. "Potbelly, rabbit teeth, knock knees - I could never seem to get it right and it haunted my every move".
"I posed as the sassy confident one, secretly horrified and hurt by careless comments and hostility. Let's get something straight: I didn't hate what I looked like - I hated the culture that was telling me to hate it."
She added that when her career began to take off, some people celebrated her attitude "but always through the lens of 'isn't she brave? Isn't it such a bold move to show THAT body on TV?'"
However, not everyone was so open to the idea of body diversity and positivity.
"There were the legions of trolls who made high school teasing look like a damned joke with the violent threats they heaped on, the sickening insults that made me ache for teen girls like me who might be reading my comments," she said.
"Well, today this body is on the cover of a magazine that millions of women will read, without Photoshop, my thigh on full imperfect display."
Dunham finished her post with a message to everyone who criticises women's bodies on social media.
"Haters are gonna have to get more intellectual and creative with their disses in 2017 because none of us are going to be scared into muumuus by faceless basement dwellers, or cruel blogs, or even our partners and friends," she said.
"Thank you to the women in Hollywood (and on Instagram!) leading the way, inspiring and normalising the female form in every form, and thank you to @glamourmag for letting my cellulite do the damn thing on news stands everywhere today ❤️ Love you all."
The Glamour cover follows Dunham's long and at times controversial battle against digital editing.
Last March the 30-year-old publicly slammed Spanish magazine Tentaciones for featuring an image of her she believed had been photoshopped.
However, the magazine denied retouching the image and Dunham soon issued an apology over her initial claim. She suggested the prevalence of digital editing in the media had contributed to her confusion, saying: "It's a weird feeling to see a photo and not know if it's your own body anymore."
Later that month, she issued a public statement via her newsletter banning all media from using edited images of her, saying "if that means no more fashion-magazine covers, so be it".