Larne majority shareholder Kenny Bruce said: "We are delighted to have secured our number one target, with the arrival of Nathan Rooney.
“As a senior management team, we feel Nathan possesses all of the attributes we were looking for in the person who will take us forward. He is a manager who has shown that he has a clear style of play, his enthusiasm is infectious and we believe he is a brilliant leader."
Rooney, 35, has helped improve the fortunes of Magpies, including securing qualification for European club competition.
Rooney's side knocked Derry City out in the first qualifying round of the Uefa Conference League in July, 3-2 the aggregate score, before losing 8-1 over two legs to FC Copenhagen in the next round.
Two years earlier Magpies went down 4-3 on aggregate to Crusaders in the Uefa Conference League first qualifying round.
Lynch's tenure at Larne saw the Invermen clinch the first Irish League titles in their history in the form of back-to-back Premiership crowns.
He also led the east Antrim club into the league stages of a major European competition, breaking new ground for an Irish League side.
Rooney added: "The squad of players excite me a lot and I am eager to get to work on the training ground with all the experts within the backroom team and I am hoping that all the energy that we create allows us to implement, continue and enhance all the teams’ performances which wear the Larne badge.
“After seeing recent games and observing from afar you can see how hard the club works within the local community to provide a better experience for the fans and this relationship between club and fans is something which can continue to grow."