In the wake of DC Comics' success reviving superheroes in the late 1950s and early 1960s, particularly with The Justice League of America, Marvel decided to follow suit.

Editor/writer Stan Lee and freelance artist Jack Kirby created the Fantastic Four, reminiscent of the non-superpowered adventuring quartet the Challengers of the Unknown that Kirby had created for DC in 1957. Eschewing such comic-book tropes as secret identities and even costumes at first, having a monster as one of the heroes, and having its characters bicker and complain in what was later called a "superheroes in the real world" approach, the series represented a change that proved to be a great success. Marvel began publishing further superhero titles featuring such heroes and antiheroes as the Hulk, Spider-Man, Thor, Ant-Man, Iron Man, the X-Men and Daredevil, and such memorable antagonists as Doctor Doom, Magneto, Galactus, the Green Goblin, and Doctor Octopus. The most successful new series was The Amazing Spider-Man, by Lee and Ditko. Marvel even lampooned itself and other comics companies in a parody comic, Not Brand Echh (a play on Marvel's dubbing of other companies as "Brand Echh", a la the then-common phrase "Brand X").

Marvel's comics were noted for focusing on characterization to a greater extent than most superhero comics before them. This was true of The Amazing Spider-Man, in particular. Its young hero suffered from self-doubt and mundane problems like any other teenager. Marvel superheroes are often flawed, freaks, and misfits, unlike the perfect, handsome, athletic heroes found in previous traditional comic books. Some Marvel heroes looked like villains and monsters. In time, this non-traditional approach would revolutionize comic books.

Comics historian Peter Sanderson wrote that in the 1960s, "DC was the equivalent of the big Hollywood studios: After the brilliance of DC's reinvention of the superhero... in the late 1950s and early 1960s, it had run into a creative drought by the decade's end. There was a new audience for comics now, and it wasn't just the little kids that traditionally had read the books. The Marvel of the 1960s was in its own way the counterpart of the French New Wave.... Marvel was pioneering new methods of comics storytelling and characterization, addressing more serious themes, and in the process keeping and attracting readers in their teens and beyond. Moreover, among this new generation of readers were people who wanted to write or draw comics themselves, within the new style that Marvel had pioneered, and push the creative envelope still further."

Lee became one of the best-known names in comics, with his charming personality and relentless salesmanship of the company. His "voice" permeates the stories, the letters and news pages, and even the hyperbolic house ads of many of the Marvel Comics of the first half of the 1960s: his sense of humor and generally lighthearted manner, and the exaggerated depiction of the Bullpen (Lee's name for the staff) as one big, happy family. The artists — who eventually co-plotted the stories based on the busy Lee's rough synopsis or even simple spoken concept, in what became known as the Marvel Method — contributed greatly to Marvel's product and success. Kirby in particular is generally credited for many of the cosmic ideas and characters of Fantastic Four and The Mighty Thor, such as the Watcher, the Silver Surfer and Ego the Living Planet, while Steve Ditko is recognized as the driving artistic force behind the moody atmosphere and street-level naturalism of Spider-Man and the surreal atmosphere of Doctor Strange. Lee, however, continues to receive credit for his well-honed skills at dialogue and story sense, for his keen hand at choosing and motivating artists and assembling creative teams, and for his uncanny ability to connect with the readers. These included nickname endearments in the credits and in the monthly "Bullpen Bulletins" and letters pages, with readers given humanizing hype about the likes of artists and writers "Jolly Jack Kirby", "Rascally Roy Thomas", "Jazzy Johnny Romita" and others, right down to letterers "Swingin' Sammy Rosen" and "Adorable Artie Simek".

Lesser-known staffers during the company's industry-changing growth in the 1960s (some of whom worked primarily for Marvel publisher Martin Goodman's umbrella magazine corporation) included circulation manager Johnny Hayes, subscriptions person Nancy Murphy, bookkeeper Doris Siegler, merchandising person Chip Goodman (son of publisher Martin) and Arthur Jeffrey, described in the December 1966 "Bullpen Bulletin" as "keeper of our MMMS [Merry Marvel Marching Society] files, guardian of our club coupons and defender of the faith".

In the fall of 1968, company founder Goodman sold Marvel Comics and his other publishing businesses to the Perfect Film and Chemical Corporation. It grouped these businesses in a subsidiary called Magazine Management Co. Goodman remained as publisher.