Many of the reactions were positive with some calling the magazine brave and lauding the move as historic.
Others couldn't even see what the big deal was.
However some people were not so supportive and criticised the magazine for featuring Avery on the cover.
In an editor's note, magazine chief Susan Goldberg said thousands of people have weighed in "with opinions, from expressions of pride and gratitude to utter fury" since the cover was uploaded across its social media platforms.
The editor-in-chief also revealed some have even threatened to cancel their subscriptions over the move.
"Avery was able to capture the complexity of the conversation around gender," Goldberg wrote. "We thought that, in a glance, she summed up the concept of 'Gender Revolution'."
Goldberg wrote that Avery, from Kansas City, was just one of the many stories which focused on gender and how far society has come on this issue as well as those of genital mutilation, child marriage, sexual assault.
While National Geographic has featured celebrities and scientists in the past it is the first time it has featured a transgender person on the cover, The Washington Post reported.
It wouldn't be the first time, however that a transgender person has graced the cover of a magazine.
Just last year Caitlyn Jenner made her public debut on the cover of Vanity Fair.
