The 23-year old has made 155 appearances in his six seasons at the club, scoring six times for the Candy Stripes and played his final game for the club in last Thursday night's Uefa Europa Conference League second leg tie in Riga.
The Armagh native, signed by Kenny Shiels, travelled to Bolton this morning and after successfully completing his medical, put the final touches to his contract with the club.
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"On behalf of the management, players and staff at Derry City I want to put on record our thanks to Eoin for his service to the club” said the City boss.
“He has been an absolute pleasure to work with both as a player and a captain. I want to wish him every success at his new club and in his career going forward."
He has been confirmed as Bolton's fourth signing made this summer for the club's first team and has put pen to paper on a three-year-deal at the University of Bolton Stadium and joins for an undisclosed fee.
Wanderers boss Ian Evatt said: "It’s been well documented how in-depth we are with our recruitment process and how we identity position specifics in players and if their attributes fit how we want them to play.
“Eoin ticks all of those boxes. He’s a young player with a huge amount of experience – albeit in a different division; captain of a top-division team in Ireland, who has played European football and who has vast attributes we feel we can improve on.
“We know he’s got good versatility and as coaches we feel we can still improve him and he will get time to settle."