The versatile 30-year-old is a fan favourite at the Super 6 Stadium since arriving in 2015.
In a heartfelt farewell on the club's website, Magnay announced he was leaving this afternoon.
"It is with great sadness that I announce I have left Hartlepool United," he said.
It is regrettable that my season came to an end early and I was not able to play an influential role on the pitch in what is now known as my final season with the club.
"I have played for the club through arguably the toughest period in its history, I have felt the pain and frustration along with the fans but have faced the challenges head on with them.
He continued: "Whatever the opinions are of my time with Hartlepool, I can categorically state that whenever I stepped onto the pitch I did so with pride, particularly as captain, and always gave 100% whether my performance was good, bad or indifferent."
Pools boss Craig Hignett added: “During my two spells here as Manager he’s been spot on – a great professional on and off the pitch who looked after himself well and was everything you’d want in a player, he was top class.
“I am sorry to see him go but he’s been a pleasure to work with so we wish him well in whatever he does next and he knows he will always be welcome back at the football club.”
Hartlepool get their 2019/20 season underway against Sutton United on August 3.
You can find a full fixture list for Hartlepool United by clicking here.