He is known best for his prolific collection of Star Wars books, chiefly the Thrawn trilogy, and has published several other series of sci-fi and fantasy novels of his own original creation, in addition to many works of short fiction.

Lucasfilm at times used some of the more detailed Star Wars: The Roleplaying Game supplements from West End Games as references, and West End sent boxes of their sourcebooks to Zahn when he started work on a new Star Wars novel trilogy.

[4]: 193 The Thrawn trilogy marked a revival in the fortunes of the Star Wars franchise, bringing it widespread attention for the first time in years; all three Thrawn trilogy novels made The New York Times Best Seller list,[5] and set the stage and tone for most of the franchise's expanded universe content.

In 2014 Zahn collaborated with David Weber on the Manticore Ascendant series set within the Honorverse.

In 2023, Dave Filoni confirmed during the Star Wars Celebration Europe that Zahn served as a creative consultant for the Disney+ miniseries Ahsoka in order to assist the creative team in writing Thrawn correctly, as Filoni felt that only Zahn could advise them with the "right" way to adapt Thrawn as the character's creator.