Jacksonville lost its last five games, including Sunday's 38-20 defeat by Tennessee, and tied the Kansas City Chiefs for the worst record in the NFL. Tie-breaking formulas leave the Chiefs with the No. 1 overall choice in the 2013 NFL draft, however.
Jacksonville team owner Shahid Khan issued a statement Monday saying he'd met with Smith to inform him of the change and thanked him for his help during Khan's first season of owning the team.
"Gene is a good man with a long career ahead of him in football and I know this season was as difficult for him as anyone in our organization," Khan said in his statement. "I sincerely wish Gene and his family the very best today and always."
Smith, who marked his 49th birthday Monday, has been with the Jaguars since 1994 when he joined the franchise as a college scout. He became the team's first general manager in January 2009.
Smith hired Jacksonville Coach Mike Mularkey last January. It was unknown if Mularkey would be retained for next season.