The announcement came this week after DC, the creators of Superman, Batman and other graphic novels, struck a deal to make the downloadable version available only on Amazon's Kindle.
"We will not stock physical books in our stores if we are not offered the available digital format," Barnes & Noble Chief Merchant Jaime Carey said in a written statement.
The Los Angeles Times said company policy is not to stock any book that can't also be loaded into the Barnes & Noble Nook e-reader.
"To sell and promote the physical book in our store showrooms and not have the ebook available for sale would undermine our promise to Barnes & Noble customers to make available any book, anywhere, anytime," Carey said.
All is not lost for superhero fans. The Hollywood Reporter said DC's graphic novels can be purchased on the Barnes & Noble Web Site.
DC added it was disappointed at the chain's decision but had plenty of online and physical outlets for its novels.