Verheiden's introduction into writing comics came in June 1987, when he penned The American, which was published by Dark Horse Comics in its second year of operation. Starting in March of the following year, he wrote what was to be the first of many Verheiden/Dark Horse comics based on the 20th Century Fox film-series Aliens, and comics based on the similarly licensed property Predator soon followed.

In January 1989, he wrote the first of several stories featuring Superman for DC Comics' then-weekly title Action Comics, from #635. He has also written stories featuring popular icons like The Phantom, and contributed to the lauded A1 anthology. This was followed by Stalkers, a 12 issues series for Marvel Comics' Epic Comics imprint.

Verheiden has also contributed to scripts for the feature films The Mask, Timecop (he also wrote the Dark Horse comics adaptation of the film) and for the Smallville television-show. He was also supervising, then co-executive producer for Smallville during the first three seasons, as well as one of the writers on DC's Smallville comic, based on the series.

Verheiden was also the creator/writer and supervising producer on the ABC television series Timecop, and consulting producer on the UPN series The Strip.

His Phantom stories featured in a 13-issue maxi-series from DC Comics (following a 4-issue Peter David written mini-series) and took on 'real-world issues', such as poisoning, illegal weapon trading, racism, and toxic dumping. The stories usually took a more psychological approach than the Lee Falk written comic strips. Luke McDonnell was the regular artist.

Verheiden was a writer and co-executive producer on the television series Battlestar Galactica since season two, and wrote nine episodes of the series.

In 2007, Verheiden began work on the live-action screenplay for a Teen Titans film for Warner Bros., as well as an adaptation of his own Ark (written for Dark Horse Presents in the mid-1990s) with Sony Pictures.

In the mid-2000s, Dark Horse Comics gained the Evil Dead comics licence, and from January—April 2008, Verheiden wrote the four-issue miniseries based on the Sam Raimi movie, with art by John Bolton. Verheiden was no stranger to the Evil Dead team, having previously worked with Raimi on Time Cop, written a pilot for Rob Tapert and produced the screenplay for Bruce Campbell's My Name is Bruce.

In 2008, Verheiden joined the staff of Heroes as writer and consulting producer. He wrote two episodes of the season three "Fugitives" storyline. He returned to Heroes for season four as writer and consulting producer, rejoining the staff with episode 407 and co-writing episodes 410 and 417.

In 2008, Verheiden wrote "Rebirth", the first regular-series episode of Caprica, the prequel to Battlestar Galactica. The episode aired in January 2010.

In 2009, DreamWorks announced Verheiden was writing Quatermain, a live action feature project.

In 2010, Verheiden joined the staff of the television series Falling Skies as writer and co-executive producer.