The as-yet-untitled film is being directed by Zack Snyder.
The casting of Eisenberg and Irons was announced by Greg Silverman, president of creative development and worldwide production, and Sue Kroll, president of worldwide marketing and international distribution for Warner Bros. Pictures.
"Lex Luthor is often considered the most notorious of Superman's rivals, his unsavory reputation preceding him since 1940," Snyder said in a statement.
"What's great about Lex is that he exists beyond the confines of the stereotypical nefarious villain. He's a complicated and sophisticated character whose intellect, wealth and prominence position him as one of the few mortals able to challenge the incredible might of Superman," Snyder said.
"Having Jesse in the role allows us to explore that interesting dynamic, and also take the character in some new and unexpected directions. As everyone knows, Alfred is Bruce Wayne's most trusted friend, ally and mentor, a noble guardian and father figure. He is an absolutely critical element in the intricate infrastructure that allows Bruce Wayne to transform himself into Batman. It is an honor to have such an amazingly seasoned and gifted actor as Jeremy taking on the important role of the man who mentors and guides the guarded and nearly impervious facade that encapsulates Bruce Wayne."
Starring Henry Cavill as Superman and Ben Affleck as Batman, the film is set for release in 2016.