The magazine, which has only been available in print for the last three months, previously featured an interview with the 19-year-old model in its April edition, but have now chosen her to grace the front page.
Aden also wears another item that is unusual to see on a Vogue model: braces.
She spoke about why the opportunity was so important to her in a video on her Instagram.
“Every little girl deserves to see a role model that’s dressed like her, resembles her, or even has the same characteristics as her,” she said.
“I think beauty is for everyone and I think everyone can look beautiful. You just have to be confident.”
Aden was first propelled into the limelight in November 2016, as the first contestant to wear a hijab and Burkini during the Miss Minnesota USA pageant.
She then went on to star in Kanye West’s Yeezy season 5 show less than four months later.
Now signed with IMG models in New York, Aden previously told Vogue that she wants her career to help people see that women in hijabs are no different to other women.
“When I’m walking the runway I want people to see that, yes, I’m wearing a hijab – but I’m also a million other things,” she said.
“I want us to get to a place where we just see women.”
The decision to put Aden on the cover has been met with a far more positive reception than the Arabian edition’s debut cover star Gigi Hadid, who is half-Palestinian, a move that was widely criticised for cultural appropriation.
One commentator wrote on Vogue Arabia’s Instagram page: “Middle Eastern influencers deserve at least some recognition. This would have been the perfect platform for them.”
Another wrote: “Couldn’t find a proud Arab for the cover?” While another Instagram user said: “[Gigi] only mentions her Arab side to escape the cultural appropriation or when it benefits her lol.”
The June edition of Vogue Arabia will be available on newsstands across the Middle East and North Africa, as well as in select places in London, and Paris from today.