The X-Men: First Class actor is the latest to join the cast of the long-announced project, The Playlist reports. Gabriel Byrne, Colin Farrell and Cillian Murphy are also lined up to appear in the movie.
Gleeson, who plays Mad-Eye Moody in the Harry Potter series, bought the rights to the Flann O'Brien book approximately seven years ago.
At-Swim-Two-Birds tells the story of a university student writing a novel that is populated with characters from his own life.
Fassbender was previously attached to Danny Boyle's Trance, but dropped out due to scheduling conflicts.
The 34-year-old is currently shooting Ridley Scott's Prometheus opposite Noomi Rapace, Idris Elba and Ben Foster.
At-Swim-Two-Birds is scheduled to begin filming in the spring of next year.