The history of independent comics emerged from the 1960s underground comix movement, which was a countercultural reaction to the mainstream superhero narratives and the industry's self-imposed censorship from the Comics Code Authority. Underground comix, or "comix" with an "x" to distinguish them from mainstream books, were distributed in head shops and independent bookstores. Led by creators like Robert Crumb and Gilbert Shelton, these works explored themes of drug use, sexuality, and anti-establishment politics that were off-limits to corporate publishers. This spirit of artistic freedom allowed for a wider range of expression, though the movement began to decline in the mid-1970s as many of its central issues became legally challenged and its distribution network eroded.

Following the underground movement's peak, the independent comics scene grew in the late 1970s and 1980s, fueled by the rise of the direct market and dedicated comic book stores. This "alternative" era continued to offer a variety of genres and artistic styles outside the superhero formula. Publishers like Eclipse Comics and Fantagraphics Books provided platforms for creators to own their work and serialize personal stories. The 1984 success of Teenage Mutant Ninja Turtles by Kevin Eastman and Peter Laird, created by two independent artists, sparked a "black-and-white explosion" of independent titles and a speculative market boom. During this time, creators like Art Spiegelman, who had worked in underground comix, serialized his groundbreaking graphic novel Maus.

The independent comics industry was reshaped in the 1990s and beyond, influenced by the market crash of the mid-90s, which forced publishers to focus more on quality than speculation. A major event was the 1992 exodus of several star artists “Jim Lee, Todd McFarlane, Rob Liefeld, Marc Silvestri, Erik Larsen, Jim Valentino, and Whilce Portacio” from Marvel to found Image Comics, proving that creator-owned works could find mainstream commercial success. In the 21st century, the independent scene expanded further with the growth of digital publishing and crowdfunding, which have democratized the process of creating and distributing comics. Platforms like Kickstarter, alongside a thriving small press and webcomic scene, have made it easier than ever for creators to connect directly with their audience and retain ownership of their intellectual property.