Immonen studied at Toronto's York University, pursuing a career in art.
In 1988, he self-published a series called Playground; it was his first published work. He worked at several smaller comic book companies before being hired by DC Comics and Marvel Comics in 1993. Since then, Immonen has drawn such high-profile characters as Superman, Hulk, the Legion of Super Heroes, and the X-Men. His recent work includes stints on the titles Ultimate Fantastic Four and Ultimate X-Men with writers Warren Ellis and Brian K. Vaughan, as well as a 12-issue run pencilling Nextwave, which again paired him with Warren Ellis.
Stuart Immonen has also done work for Top Cow and Image Comics.
In 2005, Immonen published 50 Reasons to Stop Sketching at Conventions, a series of fifty comics that detail why he no longer does sketches for fans. Besides self-publishing, Immonen also maintains a webcomic called Never as Bad as You Think which is co-authored by his wife, Kathryn.
On October 23, 2006, Immonen was confirmed as the new artist on Marvel Comics Ultimate Spider-Man starting with issue #111. After USM #133, he will depart from that series and begin work on New Avengers, starting with issue #55 and ending with issue #64. He will however continue to be the series artist when New Avengers relaunches under the heroic age.
2010 sees the release of Moving Pictures - a webcomic co-authored by Kathryn Immonen - as a graphic novel published by Top Shelf Productions.