His first move will be deciding the fate of coach Mike Mularkey.
Owner Shad Khan tabbed the 38-year-old Caldwell on Tuesday, a day after a third interview. FoxSports.com first reported that the Jaguars had reached an agreement with Caldwell. A formal new conference is scheduled for Thursday afternoon.
"We got our man," Khan said in a statement. "I have a lot of faith in David Caldwell and I can assure our fans that the best days for the Jacksonville Jaguars are in front of us."
Added Caldwell, who chose the Jaguars over the New York Jets: "I am thrilled to accept the offer to become the next general manager of the Jacksonville Jaguars. There are no bad GM opportunities in the NFL, but to work on behalf of a dynamic owner in a rabid football city like Jacksonville is truly special. This is where I wanted to be and I could not be happier. I can't wait to get to Jacksonville and get started."
Caldwell's first task will be to make a decision on Mularkey, who went 2-14 in his first season in Jacksonville and has lost 20 of his last 23 games as a head coach.
Khan gave Mularkey's assistants permission to search for other jobs last week, an indication that he doesn't expect to retain Mularkey or his staff.
Then again, Caldwell and Mularkey have a relationship stemming from their time in Atlanta.
Before becoming the Falcons' director of player personnel in 2012, Caldwell spent four seasons as Atlanta's director of college scouting—the same four years Mularkey served as offensive coordinator. Caldwell replaced Les Snead, who was hired as St. Louis' general manager last offseason.
"He's a great guy, a great family man, does a good job," Mularkey said of Caldwell last month. "He had some experience in Indy before he got to Atlanta, and I thought he did a good job up there. ... I thought that (he would become a GM) when I worked with him, that he was heading in that direction."
Caldwell was part of an Atlanta front office that drafted quarterback Matt Ryan, linebackers Curtis Lofton and Sean Witherspoon, offensive tackle Sam Baker, safety William Moore, receiver Julio Jones and running back Jacquizz Rodgers.
He doesn't inherit as much talent in Jacksonville, but the Jaguars have the No. 2 pick in April's draft and plenty of room under the salary cap to make moves. And coming off the worst season in franchise history, it won't take much to show improvement.
Khan fired general manager Gene Smith last week, parting ways with the guy who built a team that failed to make the playoffs the last four seasons.
Smith had been with the team since its inception in 1994, working his way up from regional scout to general manager. He had been GM since 2009, compiling a 22-42 record. Not one player he acquired made the Pro Bowl, though.
Smith changed the way Jacksonville approached personnel moves. He made character as important as ability, but it never paid off the way he envisioned.
Finding talent was the main issue.
Smith whiffed on offensive tackle Eben Britton (39th overall pick in 2009), defensive tackle Tyson Alualu (10th pick in 2010) and quarterback Blaine Gabbert (10th pick in 2011). Smith traded up to select Gabbert even though several teams with quarterback needs passed on the former Missouri starter.
Smith's most controversial act came in April, when he chose punter Bryan Anger in the third round (70th pick). Anger was terrific as a rookie, but adding him never seemed like the best call for a team that needed talent and depth at so many other positions.
Smith did hit on some players, including left tackle Eugene Monroe (eighth pick in 2009), cornerback Derek Cox (73rd pick in 2009) and receivers Cecil Shorts (114th pick in 2011) and Justin Blackmon (fifth pick in 2012). But none of those starters has become a star. And Smith gave up a second-round pick to get Cox and a fourth-rounder to trade up and get Blackmon.
Caldwell will need to do better to help get the Jaguars back in the playoffs for the first time since 2007.