* The Punisher Kills the Marvel Universe (with Dougie Braithwaite, 1995, tpb, 2000 ISBN B0006RK6AQ)
* The Punisher: Welcome Back Frank (with Steve Dillon, Marvel Knights, 12 issue mini-series, 1999, tpb, 2001 ISBN 0-7851-0783-5)
* The Punisher Meets Painkiller Jane (with Joe Jusko & Dave Ross, 2001)
* The Punisher (Marvel Knights series) (with Steve Dillon, 2001-2003)
o Army of One (tpb collects #1-6, 2002 ISBN 0-7851-0839-4)
o issue #7 (contains a one-page back-up story by Ennis; #8-12 have no Ennis)
o Business As Usual (tpb collects #13-18, 2003 ISBN 0-7851-1014-3)
o Full Auto (tpb collects #20-27, 2003 ISBN 0-7851-1149-2)
o Streets of Laredo (tpb collects #19, 27-32, 2003 ISBN 0-7851-1096-8)
o Confederacy of Dunces (tpb collects #33-37, 2004 ISBN 0-7851-1344-4)
* Marvel Knights Double Shot #1: "Roots" (with Joe Quesada, 2002)
* Born (with Darick Robertson, Marvel, 4 issues, 2003, tpb, ISBN 0-7851-1025-9)
* Punisher: Countdown (with Steve Dillon & Jimmy Palmiotti, 2004, packaged with the first DVD release of the Jonathan Hensleigh's The Punisher)
* The Punisher MAX (with Leandro Fernández, Lewis Larosa, Dougie Braithwaite, Goran Parlov 2004-2008)
o In the Beginning (tpb collects #1-6, 2004, ISBN 0-7851-1391-6)
o Kitchen Irish (tpb collects #7-12, 2004, ISBN 0-7851-1539-0)
o Mother Russia (tpb collects #13-18, 2005, ISBN 0-7851-1603-6)
o Up Is Down, Black Is White (tpb collects #19-24, 2005, ISBN 0-7851-1731-8 )
o The Slavers (tpb collects #25-30, 2006, ISBN 0-7851-1899-3)
o Barracuda (tpb collects #31-36, 2006, ISBN 0-7851-2023-8)
+ Barracuda (5-issue mini-series, spin-off, tpb, Punisher Presents: Barracuda Max, September 2007, ISBN 0-7851-2465-9)
o Man of Stone (tpb collects #37-42, May 2007, ISBN 0-7851-2165-X)
o WidowMaker (tpb collects #43-49, September 2007, ISBN 0-7851-2544-2)
o Long, Cold, Dark (tpb collects #50-54)
o Valley Forge, Valley Forge (tpb collects #55-60)
o From First to Last (tpb, 152 pages, hardcover, December 2006, ISBN 0785122761, paperback, July 2007, ISBN 0-7851-1715-6) collects:
+ "The End" (with Richard Corben, 2004)
+ "The Cell" (with Lewis Larosa, 2005 )
+ "The Tyger" (with John Severin, 2006)