Mr Trudeau appears on the cover of an issue of Marvel's "Civil War II: Choosing Sides", released on Wednesday.
Clad in a Maple-leaf tank top, boxing gloves and shorts, he is surrounded by members of a Canadian superhero group.
In the story, he appears to advise the superhero team.
Toronto-based cartoonist Ramon Perez told the BBC he chose to depict Mr Trudeau in boxing gear to showcase his unique personality.
"Rather than do a stuffy suit and tie rendition of our [prime minister], I wanted to bring forth more of his personality," Mr Perez said.
"He has a very youthful demographic and is present in social media. As well, he has a boxing history, and boxing itself being a part of the short story he appears in, it was the perfect fit."
Mr Trudeau is approached by Alpha Flight, Canada's premiere superhero team, in the story. The group, representatives of Canada globally in the comic book, asks for his advice on a political situation happening in the Marvel universe.
Writer Chip Zdarsky of Edmonton told the Canadian Press he included Mr Trudeau in the story because he "seems to be the popular culture association with Canada right now".
The Prime Minister's Office told Mr Zdarsky that they could not endorse the comic but were okay with Mr Trudeau being featured.
"It's a little tricky just because once you start to put words in the prime minister's mouth, we acknowledge that this is basically Trudeau fan fiction," Mr Zdarsky said.
"I had to kind of think about where he would stand on something like that and how he would handle it. Hopefully, I did a good job. Maybe I'll get a call from him saying: 'How could you have me saying that to... Iron Man?"'
Mr Trudeau's all-action role has not been confined to the pages of fiction - he was photographed in June jogging in Ottawa with Mexican President Pena Nieto when the two countries held bilateral talks.
Canadian Prime Minister Justin Trudeau has been a boxer, a nightclub bouncer, a world leader - and now, a cartoon book character.