On 28 July 2009, Napoli have signed the striker on a five-year deal, for €5 million. He scored his first goal with the partenopei on 16 August 2009 in the Coppa Italia match Napoli-Salernitana (3–0).
During the U-20 World Cup in Canada, Hoffer shaved the name "Jimmy" into one side of his head after receiving that nickname from a coach. The nickname is a reference to Jimmy Hoffa.
He was part of the Austrian squad that played at Euro 2008, a competition which Austria co-hosted along with Switzerland. The only match that Hoffer started in was their last group match against Germany in Vienna.