Chairman Paul Scally revealed the club was forced to "reluctantly agree to terminate his contract" after the 47-year-old made it clear he wished to make a return to management.
Hessenthaler had stepped down as manager of Gillingham a year ago after failing to reach the play-offs, and he moved upstairs into his new role but following the Gills' promotion back to League One under Martin Allen, the former Watford midfielder has decided to step down.
In a statement on the club's website, Scally said: "After lengthy discussions over the past few days with Andy Hessenthaler, and having refused him permission over the past few months in speaking to other clubs interested in employing him in coaching/management capacities, I have reluctantly agreed to terminate his contract with the club forthwith to allow him to explore these opportunities, and return to football management.
"Andy has made a huge contribution to this football club over the past years, and played a major role in the club achieving the success of this season past, working tirelessly behind the scenes in assisting myself and the team management with a fantastic Championship winning promotion to League One.
"I have long been conscious of Andy's desire to return to the training ground in coaching or management capacities, areas in which he has had great success over the past few years, and I know I speak for everyone connected to Gillingham Football Club when I wish him every success in the future.
"He will always be a welcome guest here at Priestfield, and no doubt will be building another successful team, challenging for a promotion in the not too distant future."
During his playing career with the club, Hessenthaler made 391 appearances, including a four-year spell as player/manager between 2000 and 2004.
He returned to concentrating solely on his playing career again until 2006, before returning to the managerial hotseat in 2010.
- Sports & Recreation
- Andy Hessenthaler
- League One