Eisner has been recognized for his work with the National Cartoonists Society Comic Book Award for 1967, 1968, 1969, 1987 and 1988, as well as its Story Comic Book Award in 1979, and its Reuben Award in 1998. In 1975, he was awarded the Inkpot Award and the second Grand Prix de la ville d’Angoulême.

He was inducted into the Academy of Comic Book Arts Hall of Fame in 1971, and the Jack Kirby Hall of Fame in 1987. The following year, the Will Eisner Comic Industry Awards were established in his honor. In 2015, Eisner was posthumously elected to the Society of Illustrators Hall of Fame.

Comics by Will Eisner are archived in the James Branch Cabell Library of Virginia Commonwealth University. VCU’s James Branch Cabell Library has served as the repository for the Will Eisner Comic Industry Awards since 2005. Each year following Comic-Con, nominated and award-winning titles are donated to the library’s Special Collections and Archives and made available to researchers and visitors. Approximately 1,000 comic books, graphic novels, archival editions, scholarly titles, and journals are included in the VCU library’s expansive Comic Arts Collection.

On the 94th anniversary of Eisner’s birth, in 2011, Google used an image featuring the Spirit as its logo.

With Jack Kirby, Robert Crumb, Harvey Kurtzman, Gary Panter, and Chris Ware, Eisner was among the artists honored in the exhibition “Masters of American Comics” at the Jewish Museum in New York City, from September 16, 2006, to January 28, 2007. In honor of Eisner’s centennial in 2017, Denis Kitchen and John Lind co-curated the largest retrospective exhibitions of Will Eisner’s original artwork, shown simultaneously at The Society of Illustrators in New York City and Le Musée de la Bande Dessinée in Angoulême, France. Both exhibitions were titled Will Eisner Centennial Celebration and collectively over 400 original pieces were included. A catalogue of the same name was released by Dark Horse Books and nominated for multiple Eisner Awards in 2018.