In the early 1970s, Stern and Bob Layton published the fanzine CPL (Contemporary Pictorial Literature), one of the first platforms for the work of John Byrne. CPL rapidly became a popular fan publication, and led to the two forming an alliance with Charlton Comics to produce and publish "the now-famous Charlton Bullseye magazine." During the mid-1970s, both Marvel and DC were publishing in-house "fan" publications (F.O.O.M. and The Amazing World of DC Comics respectively), and Charlton wished to make inroads into the superhero market, as well as "establish a fan presence," leading to the alliance with CPL to produce the Charlton Bullseye. This led to Charlton giving Layton and Stern "access to unpublished material from their vaults by the likes of Steve Ditko, Jeff Jones and a host of others."
Stern broke into the industry as a writer in 1975 as part of the Marvel Comics "third wave" of creators, which included artists Byrne and Frank Miller, and writers Jo Duffy, Mark Gruenwald and Ralph Macchio.
Stern worked briefly as an editor (notably on The Uncanny X-Men), but is better known for a brief run with John Byrne on Captain America and for his lengthy stints on The Amazing Spider-Man,Doctor Strange, and The Avengers. In 1982, he co-created Marvel's second Captain Marvel and the Hobgoblin, both with artist John Romita Jr.. In 1984, Stern co-created the Avengers spin-off West Coast Avengers, with artist Bob Hall.
In 1987, after a dispute with editor Mark Gruenwald over upcoming storylines, Stern was fired from The Avengers. He began freelancing for DC Comics, where he was one of the core Superman writers for almost a decade (working on Superman and Action Comics), during which he helped to devise the "Death of Superman" storyline that revived interest in the character in the mid-1990s. Stern also wrote a relaunched Atom series and co-created the 1980s Starman series starring the Will Payton version of the character, with artist Tom Lyle for DC.
In 1996, Stern returned to Marvel to write the miniseries Spider-Man: Hobgoblin Lives, and contributed to three issues of Spectacular Spider-Man in 1998 which featured the first confrontation between Norman Osborn and Roderick Kingsley. Over the next four years, he wrote the short-lived Marvel Universe series, as well as such miniseries as Avengers Two, Avengers Infinity, and Spider-Man: Revenge of the Green Goblin. Stern also collaborated with Avengers writer Kurt Busiek on Iron Man and the miniseries Avengers Forever, and with Byrne on The Lost Generation.
Stern has also written a number of graphic novels, including Doctor Strange & Doctor Doom: Triumph and Torment; Superman for Earth; The Incredible Hulk vs. Superman; and Superman: A Nation Divided.
Since 2001, most of his comics work has been for European publishers Egmont (writing The Phantom) and Panini UK. However, 2006-2007 saw a new Darkman mini-series he had written, Darkman vs. Army of Darkness, for Dynamite Entertainment, with co-writer Kurt Busiek.
In addition to his comics work, Stern has written three novels: The Death and Life of Superman (Bantam Books, 1993), Smallville: Strange Visitors (Warner Books, 2002), and Superman: The Never-Ending Battle (Pocket Books, 2005). The Death and Life of Superman was a New York Times bestseller in hardcover and was released as a mass market paperback in 1994; a new trade paperback edition was released by Barnes & Noble Books in 2004.
Stern married Cornell University chemistry teacher Carmela Merlo in Ithaca, New York, in June 1982, at a ceremony attended by many Marvel staffers, including editor-in-chief Jim Shooter.