Many of the concepts and even characters created by Scott Lobdell and fellow X-Men Writer Fabian Nicieza were used throughout the run of the popular 1990s X-Men: The Animated Series. Lobdell is even referenced in episode #46 of the show, "One Man's Worth", where he poses as a human used to fuel Trevor Fitzroy's mutant power to travel through time. The scene shows Master Mold saying "Lobdell, I have a job for you." He is then grabbed by Fitzroy, who absorbs his life Energy and creates a time portal.

His work has won him recognition in the comic books industry, such as a nomination for the Comics Buyer's Guide Award for "Favorite Writer" in 1997.

As of August 2008, Lobdell is the regular Writer for Galaxy Quest, a series published by IDW Publishing, with art by Ilias Kyriazis, centered on the eve of the relaunch of the Galaxy Quest series, now titled Galaxy Quest: The Journey Continues.

Lobdell created Paranormal Activity: The Search for Katie with art from Mark Badger it was released in December 2009 on iPhone.

In 2011, his portrayal of Starfire in the first issue of Red Hood And The Outlaws came under fire. The writing of the character was scrutinized by comics media and fans. Lobdell would later express that Kori's perceptions as an alien are not meant to be the same as humans on all things and that she will often challenge Roy and Jason Todd's views. He would also go on to say he felt the derogatory comments from readers about her portrayal were far worse than anything in the actual book and that the arc should be judged in full for a true sense of her character and that he would not "stand up in a movie theater and shout out the ending" to relieve the controversy at the cost of the story.

In 2013, Scott Lobdell apologized to comic book artist/writer MariNaomi for sexually harassing her on stage during the Prism Comics Panel at Long Beach Comic Con. MariNaomi submitted an article to XoJane discussing how she felt harassed by a fellow panelist when he questioned her sexuality on stage, made offensive comments about her appearance and Asian racial features, and made sexually inappropriate jokes about her during the panel. MariNaomi did not name her harasser, but Scott Lobdell later admitted that he was the panelist in question, and issued an apology to MariNaomi through Heidi MacDonald, chief Editor of ComicsBeat.com.

Lobdell wrote the screenplay for Blumhouse’s slasher film Happy Death Day. The film was released on October 13, 2017 by Universal Pictures.