| Year | Title | Authors | Ref. | 
| 1980s | 
| 1988 | Gumby Summer Fun Special #1 (Comico: The Comic Company) | Bob Burden and Art Adams | [1] | 
| Concrete #5 (Dark Horse Comics) | Paul Chadwick | 
| Eddy Current #1 (Mad Dog Graphics) | Ted McKeever | 
| Grendel #12 (Comico: The Comic Company) | Matt Wagner, Arnold Pander, Jacob Pander, and Jay Geldof | 
| Justice League International #1 (DC Comics) | Keith Giffen, J. M. DeMatteis, Kevin Maguire, and Terry Austin | 
| Zot! #14 (Eclipse Comics) | Scott McCloud | 
| 1989 | Kings in Disguise #1 (Kitchen Sink Press) | James Vance and Dan Burr | [2] | 
| Animal Man #5 (DC Comics) | Grant Morrison, Chas Truog, and Doug Hazlewood | 
| Batman: The Killing Joke (DC Comics) | Alan Moore and Brian Bolland | 
| Swamp Thing #75 (DC Comics) | Rick Veitch | 
| Twist #2 (Kitchen Sink Press) | Various creators | 
| 1990s | 
| 1990 | There was no Eisner Award ceremony, or awards distributed, in 1990, due to widespread balloting mix-ups.[3] | 
| 1991 | Concrete Celebrates Earth Day (Dark Horse Comics) | Paul Chadwick, Charles Vess, and Jean "Moebius" Giraud | [4] | 
| BLAB! #5 (Kitchen Sink Press) | edited by Monte Beauchamp | 
| Marshall Law: Kingdom of the Blind (Apocalypse Ltd) | Pat Mills and Kevin O'Neill | 
| Zot! #33 (Eclipse Comics) | Scott McCloud | 
| 1992 [note 1] | Sandman #22-#28 (DC Comics) | Neil Gaiman and various artists | [5] | 
| American Splendor #16 (Tundra Publishing) | Harvey Pekar and various artists | 
| Dark Horse Presents "Sin City" (Dark Horse Comics) | Frank Miller | 
| Groo the Wanderer #78 (Marvel Comics/Epic Comics) | Mark Evanier and Sergio Aragonés | 
| Swamp Thing #113 (DC Comics) | Nancy A. Collins, Thomas Yeates, and Shepherd Hendrix | 
| 1993 | Nexus: The Origin (Dark Horse Comics) | Mike Baron and Steve Rude | [6] | 
| Bloodlines: A Tale from the Heart of Africa (Epic Comics) | Cindy Goff, Rafael Nieves, and Seitu Hayden | 
| Hellblazer #56: "Diary of Danny Drake" (DC Comics) | Garth Ennis and David Lloyd | 
| Peepshow #1 (Drawn & Quarterly) | Joe Matt | 
| Sandman #40: "The Parliament of Rooks" (DC Comics) | Neil Gaiman and Jill Thompson | 
| Sandman #39: "Soft Places" (DC Comics) | Neil Gaiman and John Watkiss | 
| 1994 | The Batman Adventures: Mad Love (DC Comics) | Paul Dini and Bruce Timm | [7] | 
| Spawn #10: "Crossing Over" (Image Comics) | Dave Sim and Todd McFarlane | 
| Groo the Wanderer #100: "A Little Knowledge" (Marvel Comics) | Mark Evanier and Sergio Aragonés | 
| Marvels #2: "Monsters" (Marvel Comics) | Kurt Busiek and Alex Ross | 
| Sandman #50: "Ramadan" (DC Comics/Vertigo Comics) | Neil Gaiman and P. Craig Russell | 
| 1995 | The Batman Adventures Holiday Special (DC Comics) | Paul Dini, Bruce Timm, Ronnie del Carmen, and others | [8] | 
| Acme Novelty Library #1 (Fantagraphics) | Chris Ware | 
| Bone #16: "Eyes of the Storm" (Cartoon Books) | Jeff Smith | 
| The Dance of Lifey Death (Dark Horse Comics) | Eddie Campbell | 
| Sandman Mystery Theatre Annual #1 (DC Comics/Vertigo Comics) | Matt Wagner, Steven T. Seagle, and various artists | 
| 1996 | Kurt Busiek's Astro City" #4: "Safeguards (Jukebox Productions/Image Comics) | Kurt Busiek and Brent Anderson | [9] | 
| Acme Novelty Library #4 (Fantagraphics) | Chris Ware | 
| Bacchus Color Special (Dark Horse Comics) | Eddie Campbell and Teddy Kristiansen | 
| Eightball #16 (Fantagraphics) | Daniel Clowes | 
| Stray Bullets #3: "The Party" (El Capitan Books) | David Lapham | 
| 1997 | Kurt Busiek's Astro City vol. 2 #1: "Welcome to Astro City" (Jukebox Productions/Homage Comics) | Kurt Busiek, Brent Anderson, and Will Blyberg | [10] | 
| Giant THB Parade (Horse Press) | Paul Pope | 
| Kane #13: "Point of View" (Dancing Elephant Press) | Paul Grist | 
| Elric #0: Neil Gaiman's "One Life Furnished in Early Moorcock" (Topps) | adapted by P. Craig Russell | 
| Optic Nerve #3 (Drawn & Quarterly) | Adrian Tomine | 
| Sandman #75: "The Tempest" (DC Comics/Vertigo Comics) | Neil Gaiman and Charles Vess | 
| Stray Bullets #10: "Here Comes the Circus" (El Capitan Books) | David Lapham | 
| 1998 | Kurt Busiek's Astro City vol. 2 #10: "Show `Em All" (Jukebox Productions/Homage Comics) | Kurt Busiek, Brent Anderson, and Will Blyberg | [11] | 
| Batgirl Adventures #1 (DC Comics) | Paul Dini and Rick Burchett | 
| The Dreaming #15: "Day's Work, Night's Rest" (DC Comics/Vertigo Comics) | Jeff Nicholson | 
| Sof' Boy and Friends #1 (Drawn & Quarterly) | Archer Prewitt | 
| Superman Adventures #3: "Distant Thunder (DC Comics) | Scott McCloud, Rick Burchett, and Terry Austin | 
| 1999 | Hitman #34: "Of Thee I Sing" (DC Comics) | Garth Ennis, John McCrea, and Garry Leach | [12] | 
| The Clowns (I Pagliacci) (Dark Horse Comics) | P. Craig Russell and Galen Showman | 
| Empty Love Stories (Funny Valentine Press) | Steve Darnall and various artists | 
| From Hell: Dance of the Gull Catchers (Kitchen Sink Press) | Alan Moore and Eddie Campbell | 
| Kane #22: "Fwankie's Big Night Out" (Dancing Elephant Press) | Paul Grist | 
| 2000s | 
| 2000 | Tom Strong #1: "How Tom Strong Got Started" (America's Best Comics) | Alan Moore, Chris Sprouse, and Al Gordon | [13] | 
| I Die at Midnight (DC Comics/Vertigo Comics) | Kyle Baker | 
| Promethea #3: "Misty Magicland" (America's Best Comics) | Alan Moore, J. H. Williams III, and Mick Gray | 
| Stray Bullets #19: "Live Nude Girls!" (El Capitan Books) | David Lapham | 
| Transmetropolitan #27: "Monstering" (DC Comics/Vertigo Comics) | Warren Ellis, Darick Robertson, and Rodney Ramos | 
| 2001 | Promethea #10: "Sex, Stars and Serpents" (America's Best Comics) | Alan Moore, J. H. Williams III, and Mick Gray | [14] | 
| Finder #19: "Talisman" (Lightspeed Press) | Carla Speed McNeil | 
| Hey Mister: The Trouble with Jesus (Top Shelf Productions) | Pete Sickman-Garner | 
| Lucifer #4: "Born with the Dead" (Vertigo Comics/DC Comics) | Mike Carey, Warren Pleece, and Dean Ormston | 
| Paul in the Country (Drawn & Quarterly) | Michel Rabagliati | 
| Sock Monkey, vol. 3 #2 (Dark Horse Comics/Maverick) | Tony Millionaire | 
| 2002 | Eightball #22 (Fantagraphics) | Daniel Clowes | [15] | 
| The Fall (Drawn & Quarterly) | Ed Brubaker and Jason Lutes | 
| Finder #22: "Fight Scene" (Lightspeed Press) | Carla Speed McNeil | 
| 100 Bullets #27: "Idol Chatter" (DC Comics/Vertigo Comics) | Brian Azzarello and Eduardo Risso | 
| Optic Nerve #8: "Bomb Scare" (Drawn & Quarterly) | Adrian Tomine | 
| 2003 | The Stuff of Dreams (Fantagraphics) | Kim Deitch | [16] | 
| The Castaways (Absence of Ink) | Rob Vollmar and Pablo Callejo | 
| Fleep (Sparkplug Comics) | Jason Shiga | 
| My Friend Dahmer (Derfcity Comics) | Derf Backderf | 
| My Uncle Jeff (Origin) | Damon Hurd and Pedro Camello | 
| 2004 | Conan: The Legend #0 (Dark Horse Comics) [note 2] | Kurt Busiek and Cary Nord | [17] | 
| The Goon #1 (Dark Horse Comics) [note 2] | Eric Powell | 
| Finder #30: "Beware of Dog" (Lightspeed Press) | Carla Speed McNeil | 
| Giant THB v.2 #1 (Horse Press) | Paul Pope | 
| Global Frequency #5: "Big Sky" (WildStorm/DC Comics) | Warren Ellis and Jon J Muth | 
| Usagi Yojimbo #65: "Usagi and the Tengu" (Dark Horse Comics) | Stan Sakai | 
| 2005 | Eightball #23: "The Death Ray" (Fantagraphics) | Daniel Clowes | [18] | 
| Demo #7: "One Shot, Don't Miss" (AiT/Planet Lar) | Brian Wood and Becky Cloonan | 
| Ex Machina #1: "The Pilot" (WildStorm/DC Comics) | Brian K. Vaughan, Tony Harris, and Tom Feister | 
| Global Frequency #12: "Harpoon" (WildStorm/DC Comics) | Warren Ellis and Gene Ha | 
| The Goon #6: "Ilagarto Hombre!" (Dark Horse Comics) | Eric Powell | 
| 2006 | Solo #5 (DC Comics) | Darwyn Cooke | [19] | 
| The Bakers (Kyle Baker Publishing) | Kyle Baker | 
| Ex Machina #11: "Fortune Favors" (WildStorm/DC Comics) | Brian K. Vaughan, Tony Harris, and Tom Feister | 
| The Innocents (Fantagraphics/Coconino Press) | Gipi | 
| Promethea #32: "Wrap Party" (America's Best Comics) | Alan Moore and J. H. Williams III | 
| 2007 | Batman/The Spirit #1: "Crime Convention" (DC Comics) | Jeph Loeb and Darwyn Cooke | [20] | 
| A Late Freeze | Danica Novgorodoff | 
| The Preposterous Adventures of IronHide Tom (AdHouse Books) | Joel Priddy | 
| Skyscrapers of the Midwest #3 (AdHouse Books) | Joshua Cotter | 
| They Found the Car (Fantagraphics) | Gipi | 
| 2008 | Justice League of America #11: "Walls" (DC Comics) | Brad Meltzer and Gene Ha | [21] | 
| Amelia Rules! #18: "Things I Cannot Change" (Renaissance Press) | Jimmy Gownley | 
| Delilah Dirk and the Treasure of Constantinople | Tony Cliff | 
| Johnny Hiro #1 (AdHouse Books) | Fred Chao | 
| The Sensational Spider-Man Annual #1: "To Have or to Hold" (Marvel Comics) | Matt Fraction and Salvador Larroca | 
| 2009 | No award given out in 2009.[22] | 
| 2010s | 
| 2010 | Captain America #601: “Red, White and Blue-Blood" (Marvel Comics) | Ed Brubaker and Gene Colan | [23][24] | 
| The Brave and the Bold #28: “Blackhawk and the Flash: Firing Line" (DC Comics) | J. Michael Straczynski and Jesus Saiz | 
| Ganges #3 (Fantagraphics) | Kevin Huizenga | 
| The Unwritten #5: “How the Whale Became" (Vertigo Comics/DC Comics) | Mike Carey and Peter Gross | 
| Usagi Yojimbo #123: “The Death of Lord Hikiji” (Dark Horse Comics) | Stan Sakai | 
| 2011 | Hellboy: Double Feature of Evil (Dark Horse Comics) | Mike Mignola and Richard Corben | [25][26] | 
| The Cape (IDW Publishing) | Joe Hill, Jason Ciaramella, and Zack Howard | 
| Fables #100 (Vertigo Comics/DC Comics) | Bill Willingham, Mark Buckingham, and others | 
| Locke & Key: Keys to the Kingdom #1: “Sparrow" (IDW Publishing) | Joe Hill and Gabriel Rodriguez | 
| Unknown Soldier #21: “A Gun in Africa" (Vertigo Comics/DC Comics) | Joshua Dysart and Rick Veitch | 
| 2012 | Daredevil #7 (Marvel Comics) | Mark Waid, Paolo Rivera, and Joe Rivera | [27][26] | 
| Ganges #4 (Fantagraphics) | Kevin Huizenga | 
| Locke & Key: Guide to the Known Keys (IDW Publishing) | Joe Hill and Gabriel Rodriguez | 
| Princeless #3 (Action Lab Comics) | Jeremy Whitley and Mia Goodwin | 
| The Unwritten #24: "Stairway to Heaven" (Vertigo Comics/DC Comics) | Mike Carey, Peter Gross, and Al Davison | 
| 2013 | The Mire | Becky Cloonan | [28][26] | 
| Lose #4: "The Fashion Issue" (Koyama Press) | Michael DeForge | 
| Pope Hats #3 (AdHouse Books) | Ethan Rilly | 
| Post York #1 (Uncivilized Books) | James Romberger and Crosby | 
| Tales Designed to Thrizzle #8 (Fantagraphics) | Michael Kupperman | 
| 2014 | Hawkeye #11: “Pizza Is My Business" (Marvel Comics) | Matt Fraction and David Aja | [29][26] | 
| Demeter | Becky Cloonan | 
| Love and Rockets: New Stories #6 (Fantagraphics) | Gilbert Hernandez and Jaime Hernandez | 
| Viewotron #2 | Sam Sharpe | 
| Watson and Holmes #6 (New Paradigm Studios) | Brandon M. Easton and N. Steven Harris | 
| 2015 | Beasts of Burden: Hunters and Gatherers (Dark Horse Comics) | Evan Dorkin and Jill Thompson | [30][26] | 
| Astro City #16: “Wish I May” (Vertigo Comics/DC Comics) | Kurt Busiek and Brent Anderson | 
| Madman in Your Face 3D Special (Image Comics) | Mike Allred | 
| Marvel 75th Anniversary Celebration #1 (Marvel Comics) | Various creators | 
| The Multiversity: Pax Americana #1 (DC Comics) | Grant Morrison and Frank Quitely | 
| 2016 | Silver Surfer #11: “Never After" (Marvel Comics) | Dan Slott and Mike Allred | [31][26] | 
| A Blanket of Butterflies (HighWater Press) | Richard Van Camp and Scott B. Henderson | 
| I Love This Part (Avery Hill Publishing) | Tillie Walden | 
| Mowgli’s Mirror (Retrofit Comics/Big Planet Comics) | Olivier Schrauwen | 
| Pope Hats #4 (AdHouse Books) | Ethan Rilly | 
| 2017 | Beasts of Burden: What the Cat Dragged In (Dark Horse Comics) | Evan Dorkin, Sarah Dyer, and Jill Thompson | [32][26] | 
| Babybel Wax Bodysuit (Retrofit Comics/Big Planet Comics) | Eric Kostiuk Williams | 
| Blammo #9 (Kilgore Books) | Noah Van Sciver | 
| Criminal 10th Anniversary Special (Image Comics) | Ed Brubaker and Sean Phillips | 
| Sir Alfred #3 (Pigeon Press) | Tim Hensley | 
| Your Black Friend (Silver Sprocket) | Ben Passmore | 
| 2018 | Hellboy: Krampusnacht (Dark Horse Comics) | Mike Mignola and Adam Hughes | [33][26] | 
| Barbara (ShortBox) | Nicole Miles | 
| Pope Hats #5 (AdHouse Books) | Ethan Rilly | 
| The Spotted Stone (Sun Comics) | Rick Veitch | 
| What Is Left (ShortBox) | Rosemary Valero-O'Connell | 
| 2019 | Peter Parker: The Spectacular Spider-Man #310 (Marvel Comics) | Chip Zdarsky | [34] | 
| Beneath the Dead Oak Tree (ShortBox) | Emily Carroll | 
| Black Hammer: Cthu-Louise (Dark Horse Comics) | Jeff Lemire and Emi Lenox | 
| No Better Words (Silver Sprocket) | Carolyn Nowak | 
| The Terrible Elisabeth Dumn Against the Devils In Suits (IHQ Studio/Image Comics) | Arabson Assis, translated by James Robinson | 
| 2020s | 
| 2020 | My Favorite Thing Is Monsters (Fantagraphics) | Emil Ferris | [35][36] | 
| Coin-Op #8: Infatuation (Coin-Op Books) | Peter Hoey and Maria Hoey | 
| The Freak (AdHouse Books) | Matt Lesniewski | 
| Minotäar (ShortBox) | Lissa Treiman | 
| Sobek (ShortBox) | James Stokoe | 
| 2021 | Sports is Hell (Koyama Press) | Ben Passmore | [37][38] | 
| The Burning Hotels (Birdcage Bottom Books) | Thomas Lampion | 
| Hedra (Image Comics) | Jesse Lonergan | 
| The Other History of the DC Universe #1 (DC Comics) | John Ridley and Giuseppe Camuncoli | 
| Stanley's Ghost: A Halloween Adventure (Storm Kids) | Jeff Balke, Paul Storrie, and Dave Alvarez | 
| 2022 | Wonder Woman Historia: The Amazons (DC Comics) | Kelly Sue DeConnick and Phil Jimenez | [39] | 
| Marvel’s Voices: Identity #1 (Marvel Comics) | edited by Darren Shan | 
| Mouse Guard: The Owlhen Caregiver and Other Tales (Boom! Comics/Archaia) | David Petersen | 
| Nightwing #87: "Get Grayson" (DC Comics) | Tom Taylor and Bruno Redondo | 
| Wolvendaughter (Quindrie Press) | Ver | 
| 2023 | Batman: One Bad Day: The Riddler (DC Comics) | by Tom King and Mitch Gerads | [40] | 
| Mary Jane & Black Cat Beyond | Jed Mackay and C. F. Villa | 
| Moon Knight: Black, White, and Blood #3 (Marvel Comics) | edited by Tom Brevoort | 
| Star Trek #400 (IDW) | edited by Heather Antos | 
| A Vicious Circle Book 1 (BOOM! Studios) | by Mattson Tomlin and Lee Bermejo |