The right back reached the end of his deal with Rovers, with new boss Richie Wellens opting not to continue the pursuit of a new deal with the 25-year-old.
Halliday was among a group of players that were offered fresh terms by Rovers in March but failed to reach an agreement with the club.
It is understood he had recently expressed an interest in accepting the terms offered by Rovers but Wellens took the deal off the table.
The Rovers boss is confident he can secure an improved replacement with the funds that would have been used to cover Halliday’s contract.
Halliday joined Rovers two years ago from Cambridge United two years ago and went on to make 87 appearances, scoring once. He was ever present in all competitions for Rovers from signing until the defeat at Plymouth Argyle in October when he was subbed off for the first time.
He suffered a back injury in April which kept him out of action until the final game of the season when he came off the bench.
Halliday has signed a two-year deal with League One rivals Fleetwood.
“I’m delighted to get it done,” he told Fleetwood’s official website. “It’s been a while since the season ended so to finally get over to Fleetwood, I’m happy to get going and hopefully kick-on next season.
“There’s been a lot of interest since the end of last season, and we spoke to Simon [Grayson] and the rest of the team and to get the contract sorted is great.
“The facilities are lovely; they remind me of home. I’m originally from Redcar, a little town on the coast up in the North East so it’s like being back at home really. I’m looking forward to moving over and spending a lot of time over here.
“I’ve played a lot of games now at both League One and League Two level so I’m going into next season like any other.
"I’m an attacking full-back and I want to start adding goals and assists to my game in the upcoming season.”