Allen started 29 games the last two seasons. He missed the final two games last year because of a concussion.
The team also released third-year defensive end D'Aundre Reed, second-year defensive end Will Pericak and first-year receiver Jabin Sambrano.
Allen was originally signed as an undrafted rookie on April 26, 2010. He played in 78 games with 44 starts over five seasons. He finished with 452 tackles, 25 tackles for loss, two sacks and two forced fumbles.
The Jaguars signed free agent linebacker Dekoda Watson last month, adding him to a positional mix that includes Paul Posluszny and Geno Hayes.