She appeared in the swimsuit edition, out in May, wearing a number of different colourful burkinis.
She was born and remained at the Kakuma Refugee Camp until heading for the United States at the age of 7, SI reports.
Aden reflected on her childhood and was excited to return to Kenya, where the Sports Illustrated shoot took place.
Halima Aden returned to her home country of Kenya for the photoshoot.
The significance was not lost on Aden who said: "I keep thinking [back] to six-year-old me who, in this same country, was in a refugee camp". "So to grow up to live the American dream [and] to come back to Kenya and shoot for SI in the most handsome parts of Kenya-I don't think that's a story that anybody could make up".
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In an Instagram post, Aden thanked Sports Illustrated for being a part of the issue, saying she hopes to inspire other women. Quickly after, Aden made her runway debut during New York Fashion Week Fall 2017 as a model in Kanye West's Yeezy Season 5 show.
Sports Illustrated, which has featured Tyra Banks and Beyonce on its front pages, is an American magazine with a predominantly male readership, and there was mixed reaction to the news.
"This issue is for men to gawk at and get pleasure off these photos.The whole point of hijab is modesty and guarding your sexuality".
"We believe beauty knows no boundaries", said SI Swimsuit editor MJ Day.
The star continued, "Young Muslim women need to know that there is a modest swimsuit option available to them so they can join the swim team, participate in swim class at school, and go with their friends to the beach. Muslim girls should feel confident taking that step and doing so comfortably while wearing a burkini". The upcoming May issue of the magazine features the 21-year-old model, wearing a burkini (a full body swimsuit) and a hijab. It was a move slammed by many Muslim women at the time as sexist and Islamophobic.