Boyle originally moved to Easter Road on loan from Dundee in January and started 17 times for Hibs, scoring three goals, before suffering a knee injury at Falkirk at the start of May.
Edinburgh-born Boyle underwent successful surgery to repair his medial ligament in the summer after Hibs were beaten in the Championship play-offs by Rangers.
He said: “Obviously I was gutted to miss the play-offs because of the injury, but I’ve made good progress in my recovery and can’t wait to help Hibs push for promotion during the upcoming season.
“We’ve got a good group of players here and an excellent manager. The future looks really bright and I’m excited to be a part of it.
“I’m aiming to repay the manager’s faith in me and show the supporters what I’m capable of by putting in some consistently good performances.
“It was incredibly frustrating to suffer my injury set-back because I felt I was hitting some decent form, but I’m planning to come back stronger.”
Boyle joins Fraser Fyvie, Lewis Stevenson, Dan Carmichael and James Keatings in signing Hibernian contracts while captain David Gray agreed an extension to his deal.
Head coach Alan Stubbs said: “He is still going through his rehab process, but hopefully we’ll have him back available for selection sooner rather than later.
“Martin is another valuable addition to the squad for what promises to be an exciting season.”
Click here for Hibernian’s fixtures for the 2015/16 Championship campaign