He was the first player to sign for the club in 2011 and has made over 160 appearances, scoring nine goals.
"There is no doubt this is the right time for someone else to take on the challenge and drive the team and club forward," he told the club website.
"At times the pressure of captaining the club has been the reason for my availability for fixtures when my body and mind have not been ready."
Manager Tony Vance has yet to decide on a new captain.
"It is clear how proud he was to be captain and he fulfilled the role to an optimum level. Whilst he will no longer wear the armband for us, I don't believe his attitude and commitment will change," Vance said.
Guernsey FC finished 13th in Isthmian League South Division in 2015-16.
Defender Sam Cochrane has given up the captaincy of Guernsey FC.