In 1991, Miller started work on his first Sin City story. Serialized in Dark Horse Presents #51-62, Miller wrote and drew the story in black and white to emphasize its film noir origins. Proving to be another success, the story was released in a trade paperback. This first Sin City "yarn" was rereleased in 1995 under the name The Hard Goodbye. Sin City proved to be Miller's main project for much of the remainder of the decade, as Miller told more Sin City stories within this noir world of his creation, in the process helping to revitalize the crime comics genre.[citation needed] Sin City proved artistically auspicious for Miller and again brought his work to a wider audience without comics.

Daredevil: Man Without Fear was a miniseries published by Marvel Comics in 1993 based on an earlier film script.[citation needed] In this Miller and artist John Romita Jr. told Daredevil's origins differently than in the comics. Miller also returned to superheroes by writing issue #11 of Todd McFarlane's Spawn, as well as the Spawn/Batman crossover for Image Comics.

In 1995, Miller and Darrow collaborated again on Big Guy and Rusty the Boy Robot — a homage to Godzilla movies, Astro Boy and patriotic American films from World War II. The series was published as a two-part mini-series from Dark Horse Comics. In 1999 it became an animated series on Fox Kids. During this period, Miller became one of the founding members of the comic imprint Legend, under which many of his Sin City works were released, via Dark Horse. Also, it was during the 1990s that Miller did cover art for many titles in the Comics Greatest World/Dark Horse Heroes line.

Written and illustrated by Frank Miller with painted colors by Varley, 300 was a 1998 comic-book miniseries, released as a hardcover collection in 1999, retelling of the Battle of Thermopylae and the events leading up to it from the perspective of Leonidas of Sparta. 300 was particularly inspired by the 1962 film The 300 Spartans, a movie that Miller watched as a young boy. In 2007, 300 was adapted by director Zack Snyder into a highly successful film. In 2010, Dark Horse Comics announced that Miller will write and draw a prequel to "300" titled "Xerxes" to be released sometime in 2011.

Miller started the new millennium off with the long awaited sequel to Batman: The Dark Knight Returns for DC Comics after Miller had put past difference with D.C. aside. Batman: The Dark Knight Strikes Again was initially released as a three issue series. Miller has also returned to writing Batman in 2005, taking on the writing duties of All Star Batman and Robin the Boy Wonder, a series set inside of the Earth-31 Dark Knight Universe continuity in DC's Multiverse and drawn by Jim Lee. Miller has been vocally opposed to recent comic art attempting to give the cosmetic appearance of what some say is more realism. In an interview on the documentary Legends of the Dark Knight: The History of Batman, Miller said, "People are attempting to bring a superficial reality to superheroes which is rather stupid. They work best as the flamboyant fantasies they are. I mean, these are characters that are broad and big. I don't need to see sweat patches under Superman's arms. I want to see him fly."

Miller's stance against movie adaptations was to change after Robert Rodriguez made a short film from one of Miller's Sin City short stories. Rodriguez showed this short film to Miller, who was so pleased with the result that he approved a full-length film, Sin City. This would be Miller's second experience with the movie world, after becoming disenchanted years earlier with his experiences with RoboCop 2 and 3. The movie was released in the U.S. on April 1, 2005, using Miller's original comics panels as storyboards. Miller and Rodriguez are credited as codirectors, which Rodriguez insisted upon. Directors Guild of America rules permit only one person or "legitimate" directorial team (such as the Coen brothers) being listed as the director of a film. As a result, Rodriguez elected to resign from the Guild. The film's success brought renewed attention to Miller and to Sin City. And the 300 film did the same for 300.

At the 2006 San Diego Comic-Con, it was announced that Miller would write and direct a film version of Will Eisner's The Spirit. Upon release on December 25, 2008, The Spirit film was panned by critics and did poorly at the box office. A sequel to the film Sin City, based on the arc A Dame to Kill For, is in progress as of 2009, provisionally entitled Sin City 2.

At the 2009 San Diego Comic-Con, it was revealed that Miller has finished his first draft of what will become the sequel to 300. It has been revealed on Frank's Twitter account that the sequel is in fact a prequel and will be entitled Xerxes. The story will be set 19 years before 300

At Wondercon 2010 it was announced that Miller and Jim Lee's long delayed series All Star Batman and Robin will resume publication in February 2011 and retitled Dark Knight: Boy Wonder. Miller is currently at work on a graphic novel titled Holy Terror, about a former special ops agent ("The Fixer") taking on Al-Qaeda. This title was originally conceived with Batman as the protagonist, under the title Holy Terror, Batman.