The movie by director Zach Snyder is a sequel to "Man of Steel."
"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 in a statement. "Having Jesse in the role allows us to explore that interesting dynamic, and also take the character in some new and unexpected directions."
Eisenberg was nominated for an Oscar for his role as Facebook founder Mark Zuckerberg in "The Social Network."
The studio also announced that Jeremy Irons will take on the role of Alfred, Bruce Wayne's butler and most trusted friend.
"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 façade that encapsulates Bruce Wayne," Snyder said.
The film is set to open worldwide on May 6, 2016.