Henne's deal is worth $8 million, including $4.5 million guaranteed in the first year, a league source said.
The deal comes four days before the beginning of free agency and one day before Henne could have begun negotiations with other teams.
Henne, who signed a two-year deal worth $6.75 million with the Jaguars in 2012, started 13 games and threw for 3,421 yards and 13 touchdowns with 14 interceptions in 2013. He became the first Jaguars quarterback to throw for more than 3,000 yards in a season since David Garrard in 2009.
Henne's return could further cloud the future of Blaine Gabbert, who has struggled with injuries and inconsistency since being drafted 10th overall in 2011. Jacksonville is expected to take a quarterback with the third pick in May's draft. Gabbert won the starting job last season but started only three games because of injuries and eventually lost the starting job to Henne. Gabbert is entering the final year of his contract and his salary for 2014 is guaranteed.
The 28-year-old Henne led the Jaguars to a 4-4 record in the second half of the season after an 0-8 start and had nine TD passes and five interceptions in the final five games. And he did it without any elite weapons. He lost his best receiver (Justin Blackmon) to an indefinite suspension, didn't get much help from tight end Marcedes Lewis until the last month because of a calf injury, and lost his second-best receiver (Cecil Shorts) for the final three weeks because of a sports hernia.
Henne has a 5-14 record as a starter in two seasons with the Jaguars after spending the first four years of his career with Miami. He went 13-18 as a starter with the Dolphins.
Information from ESPN NFL Insider Adam Schefter was used in this report.