| 0 | - | cover | 1 | pencils: Jim Lee; inks: Klaus Janson; colors: Veronica Gandini | Punisher |
| 1 | - | cover reprint (on interior page) | 1 | pencils: Carl Potts; inks: Scott Williams | Punisher [Frank Castle] |
| 2 | An Eye for an Eye Chapter One Sunday in the Park | comic story | 28 | script: Carl Potts; pencils: Carl Potts, Jim Lee; inks: Jim Lee; colors: John Wellington; letters: Jim Novak | Punisher [Frank Castle]; Microchip; Hector Montoya; The Mob |
| 3 | Punishing Profiles | text article | 1 | script: Don Daley | |
| 4 | - | cover reprint (on interior page) | 1 | pencils: Carl Potts; inks: Jim Lee | Punisher; Daredevil |
| 5 | An Eye for an Eye Chapter Two: Tie a Yellow Ribbon | comic story | 26 | script: Carl Potts; pencils: Carl Potts, Jim Lee; inks: Jim Lee; colors: Gregory Wright; letters: Jim Novak | Punisher; Microchip; Daredevil; Jason Hunt; Hatsu Yakamoto; Katherine Yakamoto; Hector Montoya |
| 6 | - | cover reprint (on interior page) | 1 | pencils: Carl Potts; inks: Jim Lee | Punisher; Jason Hunt; Hector Montoya |
| 7 | An Eye For an Eye Chapter Three: A Dish Best Served Cold | comic story | 24 | script: Carl Potts; pencils: Carl Potts, Jim Lee; inks: Jim Lee; colors: Gregory Wright; letters: Jim Novak | Punisher; Microchip; Daredevil; Jason Hunt; Hatsu Yakamoto; Katherine Yakamoto; Manzo; Hector Montoya (Death) |
| 8 | - | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Carl Potts | Punisher |
| 9 | Sniper | comic story | 23 | script: John Wellington, Carl Potts; pencils: Jim Lee; inks: Scott Williams, Don Hudson; colors: Gregory Wright; letters: Ken Lopez | Punisher; Sniper |
| 10 | ... To the Death! | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Carl Potts | Punisher; Sniper |
| 11 | Crucible | comic story | 22 | script: Carl Potts; pencils: Jim Lee; inks: Scott Williams; colors: Gregory Wright; letters: Ken Lopez | Punisher; Sniper |
| 12 | Meeting For the First Time-- And Maybe the Last! | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Wolverine |
| 13 | On the Track of Unknown Animals | comic story | 22 | script: Carl Potts; pencils: Carl Potts, Jim Lee; inks: Jim Lee; colors: Gregory Wright; letters: Jim Novak | The Punisher; Wolverine; Microchip; Hatsu Yakamoto; Yuriko; Phillip |
| 14 | Survival of the Fittest! | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Carl Potts | Wolverine; Punisher |
| 15 | Endangered Species | comic story | 22 | script: Carl Potts; pencils: Carl Potts, Jim Lee; inks: Jim Lee; colors: Gregory Wright; letters: Jim Novak | The Punisher; Wolverine |
| 16 | - | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Klaus Janson; colors: Veronica Gandini | Punisher |
| 17 | Introducing: Damage | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Klaus Janson | Punisher |
| 18 | Damage | comic story | 22 | script: Carl Potts; pencils: Jim Lee; inks: Jim Lee; colors: Gregory Wright; letters: Jim Novak | Punisher; Shadowmasters [Hatsu Yakamoto; Yuriko; Manzo]; Phillip; Damage; Bunsen Burner Gang; Sunrise Assassin |
| 19 | Dreamtime with the Black Widow! | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher; Black Widow |
| 20 | Guilt Trip | comic story | 22 | script: Carl Potts; pencils: Jim Lee; inks: Jim Lee; colors: Gregory Wright; letters: Jim Novak | Punisher; Black Widow [Natasha Romanov]; Yuriko; Rikichi; Manzo; Phillip |
| 21 | Sniper's Back | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Carl Potts | Punisher; Sniper |
| 22 | Second Shot | comic story | 22 | script: Carl Potts; pencils: Jim Lee; inks: Scott Williams; colors: Gregory Wright; letters: Jim Novak | Punisher; Microchip; Sniper |
| 23 | Get Ready For-- Shock Treatment! | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Klaus Janson | Punisher |
| 24 | Shock Treatment | comic story | 19 | script: Carl Potts; pencils: Jim Lee; inks: Klaus Janson; colors: Gregory Wright; letters: Jim Novak | Punisher; Microchip; Ron Salazar |
| 25 | Scared Straight | comic story | 3 | script: Carl Potts; pencils: Jim Lee; inks: Klaus Janson; colors: Gregory Wright; letters: Jim Novak | Punisher (cameo) |
| 26 | Art Imitates Death | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher; Bushwacker |
| 27 | Contrast in Sin | comic story | 22 | script: Carl Potts; pencils: Jim Lee; inks: Al Milgrom, Don Hudson; colors: Gregory Wright; letters: Jim Novak | The Punisher; Microchip; Bushwacker; Dr. Doom; Kingpin |
| 28 | Vengeance Belongs to Bushwacker! | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher; Bushwacker |
| 29 | Confession | comic story | 22 | script: Carl Potts; pencils: David Ross; inks: Russ Heath; colors: Gregory Wright; letters: Jim Novak | The Punisher; Bushwacker; Kingpin; Dr. Doom |
| 30 | - | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher; Spider-Man [Peter Parker] |
| 31 | Blind Faith | comic story | 23 | script: Carl Potts; pencils: David Ross; inks: Russ Heath; colors: Gregory Wright; letters: Jim Novak | Punisher; Spider-Man [Peter Parker]; Microchip; Mary Jane; Kathryn Cushing; J. Jonah Jameson; Neo-Nazis |
| 32 | Non-Mutant Mayhem! | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher; Spider-Man [Peter Parker] |
| 33 | Headlines! | comic story | 24 | script: Carl Potts; pencils: David Ross; inks: Russ Heath; colors: Gregory Wright; letters: Jim Novak | Punisher; Spider-Man [Peter Parker]; Mary Jane Watson-Parker; J. Jonah Jameson; Kathryn Cushing; Glory Grant; Betty Leeds; Neo-Nazis; Adolf Hitler |
| 34 | Texas Checking Account Massacre! | cover reprint (on interior page) | 1 | pencils: Mark Texeira; inks: Mark Texeira | Punisher |
| 35 | Panhandle | comic story | 21 | script: Mike Baron; pencils: Neil Hansen; inks: Mark Texeira, Steve Biasi, Kenneth Rubenoff; colors: John Wellington; letters: Ken Bruzenak | Punisher; Microchip; Amos |
| 36 | The Punisher Takes a Vacation--And Hawaii Will Never Be the Same! | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher |
| 37 | Tropical Trouble | comic story | 22 | script: Carl Potts; pencils: Jim Lee; inks: Al Milgrom, Don Hudson; colors: Gregory Wright; letters: Rick Parker | Punisher [Frank Castle]; Microchip; Rikichi; Edith; Drug Dealers; Kingpin [Wilson Fisk] |
| 38 | - | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher |
| 39 | Kahuna | comic story | 22 | script: Carl Potts; pencils: Jim Lee; inks: Al Milgrom, Don Hudson; colors: Gregory Wright; letters: Rick Parker | Punisher [Frank Castle]; Microchip; Rikichi; Edith; Drug Dealers; Bullseye (on a computer file) |
| 40 | You've Just Rented A Jet-Ski to the Punisher. Kiss That Baby Goodbye! | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Klaus Janson | Punisher |
| 41 | Trauma in Paradise | comic story | 22 | script: Carl Potts; pencils: Jim Lee; inks: Al Milgrom, Don Hudson; colors: Gregory Wright; letters: Rick Parker | Punisher [Frank Castle]; Microchip; Rikichi; Edith; Drug Dealers |
| 42 | Punisher's Fighting Techniques | comic story | 6 | script: Roger Salick; pencils: Jim Lee; inks: Scott Williams; colors: Gregory Wright; letters: Ken Lopez | Punisher; Microchip |
| 43 | Punisher War Journal Equipment Page | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown | |
| 44 | Punisher War Journal Equipment Page | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown | |
| 45 | Punisher War Journal Equipment Page | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown | |
| 46 | Punisher's Arsenal | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown | |
| 47 | Punisher War Journal Equipment Page | illustration | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown | |
| 48 | Punisher's Arsenal | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown | |
| 49 | Punisher's Arsenal | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown | |
| 50 | Punisher's Arsenal | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown; letters: Eliot R. Brown | |
| 51 | Punisher's Arsenal | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown | |
| 52 | Punisher's Arsenal | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown | |
| 53 | Punisher's Arsenal | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown | |
| 54 | Punisher's Arsenal | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown | |
| 55 | Punisher's Arsenal | character profile | 1 | script: Eliot R. Brown; pencils: Eliot R. Brown; inks: Eliot R. Brown; letters: Eliot R. Brown | |
| 56 | - | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher |
| 57 | - | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee; letters: Cindy Emmert, Kevin Kobasic | Punisher |
| 58 | Special Wet and Wild Issue! | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher [Frank Castle]; Wolverine [Logan]; Sub-Mariner [Namor] |
| 59 | Make Way for Punisher War Journal and the Punisher Graphic Novel the Assassins' Guild | text article | 3 | script: Glenn Herdling | |
| 60 | The Punisher | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee; colors: Jim Lee | The Punisher [Frank Castle] |
| 61 | - | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee; colors: Gregory Wright | Punisher |
| 62 | - | cover reprint (on interior page) | 2 | pencils: Jim Lee; inks: Carl Potts; colors: Gregory Wright | Punisher; Wolverine |
| 63 | They Are Hunting the World's Most Deadliest Game... Each Other. | promo (ad from the publisher) | 1 | pencils: Jim Lee; inks: Carl Potts | Punisher [Frank Castle]; Wolverine [Logan] |
| 64 | Overstreet's Price Update #7 Cover | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher [Frank Castle]; Wolverine [Logan] |
| 65 | Wolverine/Punisher: A Bad Night for Ninjas | illustration | 2 | pencils: Jim Lee; inks: Jim Lee | Wolverine [Logan]; Punisher [Frank Castle] |
| 66 | I'll Make You a Punisher* (If You Make Me a Dollar!) | comic story | 1 | script: Rob Tokar; colors: Ed Lazellari | |
| 67 | Frank Castle on Transit Security | illustration | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher [Frank Castle] |
| 68 | - | illustration | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher |
| 69 | Punisher Hardcover Graphic Novel - Rules of the Game | text article | 1 | pencils: Jim Lee; inks: Jim Lee | Punisher [Frank Castle]; Nick Fury |
| 70 | Ghost Rider Takes on The Punisher Part 1 of 2 | cover reprint (on interior page) | 1 | pencils: Jim Lee; inks: Jim Lee | Ghost Rider [Danny Ketch]; Punisher [Frank Castle] |
| 71 | Punisher War Journal Original Art | illustration | 7 | pencils: Jim Lee; inks: Carl Potts | Punisher [Frank Castle]; Wolverine [Logan] |
| 72 | - | cover reprint (on interior page) | 1 | pencils: Carl Potts; inks: Scott Williams; colors: John Kalisz | Punisher [Frank Castle] |