The napkin, which is dated December 14, 2000, has a starting price of £300,000 (about $390,000). It was signed by Messi's father, Jorge Messi, as well as Carles Rexach, Barcelona's sporting director at the time.
The napkin was used to outline the terms of a deal that would bring Messi to Barcelona from his hometown club Newell's Old Boys. The deal was later formalized in a more detailed contract.
The napkin is being auctioned by Bonhams, a British auction house. The auction will take place online from March 18 to 27.
"This is one of the most exciting things I've ever handled," said Ian Ehling, Bonhams' head of books and manuscripts in New York. "Yes, it's a paper napkin, but it's the famous napkin that marks the beginning of Lionel Messi's career."
"It changed the future of FC Barcelona and Messi," he added. "It played a key role in giving millions of fans around the world some of the most magical moments in football."