He is currently a writer and executive editor at Charlton Neo Comics and Pix-C Webcomics, and a contributing author with Crazy 8 Press.

Kupperberg wrote the first comic book miniseries, World of Krypton in 1979[10][11] and co-wrote Secrets of the Legion of Super-Heroes the following year with E. Nelson Bridwell.

[12] Kupperberg was one of the contributors to the DC Challenge limited series in 1986[13] and his other mini-series include The Phantom Stranger (with Mike Mignola and P. Craig Russell), Power Girl, Peacemaker, Super Powers (with Jack Kirby), and the first comic book adaptation of He-Man and the Masters of the Universe.

He has also written movie parodies and humor for Marvel's Crazy Magazine (1977–1983), the series "Trash" for Britain's 2000 AD, with artist Nigel Dobbyn, and The Online Multipath Adventures of Superman web-animation (1998).

Since 2003, Kupperberg has written numerous non-fiction books for young adults, including: Spy Satellites, The Tragedy Of The Titanic, Astronaut Biographies: John Glenn (a Society Of School Librarians International Honor Book, 2004), Critical Perspectives On The Great Depression, The Nature Of Disease, Edwin Hubble And The Big Bang, The History Of The New York Colony, Rodeo Clowns, Origins Of The Action Heroes: Spider-Man, Cutting Edge Careers In Robotics, and In The News: Hurricanes for Rosen Publishing.

From 1991–2006, Kupperberg was on staff at DC Comics, editing such titles as The Flash, Wonder Woman, Jack Kirby's Fourth World, Impulse, Peter Cannon, Thunderbolt and others.

In 2007, he contributed to the Doctor Who short-story collection Short Trips: Destination Prague, and The Avenger Chronicles from Moonstone Books.

Kupperberg is currently executive editor of Charlton Neo and the online webcomics site, Pix-C, for which he has created numerous titles and features, including Paul Kupperberg's Secret Romances, Unusual Tales featuring N.E.O., "The Scarry Squad," "Edison Corliss' Industrial Steam and Ironworks," "Digger Graves, Paranormal P.I.," and "Blank."