The executive will team with new head coach Urban Meyer to help turn around a squad that finished 1-15 in 2020.
Jacksonville has finished in last place in the AFC South in each of the last three years and has only one winning season in the last 13 years. The lone exception came in 2017 with a shocking run to the AFC Championship Game in head coach Doug Marrone's first season, but the team followed that up with a 5-11 record in 2018.
The organization has also gone through significant turnover in the past few years. The Jaguars have traded away or cut Pro Bowlers Jalen Ramsey, Calais Campbell, Yannick Ngakoue, A.J. Bouye and Malik Jackson, while six different quarterbacks have started at least three games over the past three seasons.
The Jaguars eventually made a change with the firing of general manager Dave Caldwell in November after a 1-10 start to this season.
"Our football operation needs new leadership, and we will have it with a new general manager in 2021," owner Shad Khan said in a statement.
Caldwell had been with the organization since 2013 and had been a top decision-maker alongside Tom Coughlin, who was sacked in 2019.
The Jaguars will now go into next season with a fresh start under Baalke, who must make key decisions to fill holes at quarterback and other important spots. With the No. 1 overall draft pick and three other selections in the first two rounds, he'll have plenty of opportunities to rebuild the roster.
Baalke already has experience with the organization after spending this past season as the team's director of player personnel. He also served as the interim GM following Caldwell's departure. Before joining the Jaguars, he was the general manager of the San Francisco 49ers from 2011 through 2016, helping build a squad that reached the Super Bowl in the 2012 season.
He will now try to get the Jaguars on track toward their first championship in franchise history.