Jesse Eisenberg, 30, is most famous for his Oscar-nominated performance as Mark Zuckerberg in The Social Network.
Superman vs. Batman, which will also star Henry Cavill and Ben Affleck, is due out in 2016.
The film is being directed by Zac Snyder, who worked on the Superman reboot The Man Of Steel.
The Man of Steel, released in 2013, took the Superman franchise back to its start.
The movie was a financial success, taking more than $660-million at the worldwide box office.
Henry Cavill will reprise his role as Superman, with Ben Affleck starring as Batman.
Speaking about the latest casting news, director Zac Snyder said Jesse Eisenberg allows the film to take Lex Luthor, Superman’s most famous adversary, in “some new and unexpected directions”.
Lex Luthor was previously been played by Gene Hackman and Kevin Spacey.
Jeremy Irons will play Alfred, the butler to Bruce Wayne, Batman’s real identity.
Other stars on board include Laurence Fishburne (Perry White), Gal Gadot (Wonder Woman) and Amy Adams (Lois Lane).
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