The cover, often reserved for rock stars and top celebrities, features the 19-year-old teen suspect in a photo taken from one of Tsarnaev's social media accounts. In the photo, Tsarnaev is sporting shaggy hair and staring intently into the camera.
The headline on the cover reads, "The Bomber. How a popular, promising student was failed by his family, fell into radical Islam and became a monster."
More than 6,000 people have left comments on the legendary magazine's Facebook page, most denouncing Rolling Stone's decision to feature Tsarnaev.
"I think it's wrong to make celebrities out of these people," one person wrote on the magazine's Facebook page. "Why give the guy the cover of Rolling Stone? TIME gave Charles Manson the cover and all the magazines carried pictures of the Columbine shooters on the covers, too. Don't make martyrs out of these people."
Another person wrote, "Jeff Bauman, who lost both legs, should be on cover."
Rolling Stone published a preview of Janet Reitman's story online Tuesday, including "five revelations" uncovered in the article. One of the revelations sheds light on Tsarnaev's feelings about the 9/11 terrorist attacks:
"Jahar never spoke about 9/11. Once, though, he let slip to a high school friend that he thought the terrorist attacks could be justified, and pointed to US policies towards Muslim countries and US drone strikes and other attacks as his rationale."
The magazine says Reitman spent two months talking to "childhood and high school friends, teachers, neighbors and law enforcement agents" about Tsarnaev and the investigation into the bombing.
Tsarnaev pleaded not guilty last week to 30 counts associated with the bombing. Tsarnaev is accused of working with his older brother, Tamerlan Tsarnaev, to set off a pair of bombs near the finish line of the Boston Marathon April 15, killing three and injuring more than 260 others.