The Blues have moved quickly following the resignation of Phil Brown last week.
Chairman Lee Sharples said: “David has been a true professional since first making contacted about the managers role.
“David's desire and passion to not only work for the club but to help the club grow and succeed both on field and off field working in line with the clubs new recruitment process was a delight to hear.”
Joining Lynch in the new-look management team is Chris Holland as assistant manager and Carl Garner as director of football.
Lynch said: "I am delighted to be appointed as the new Clitheroe FC manager.
“This is a fantastic opportunity for me and I am looking forward to the challenge ahead.
“As previous club captain I understand the passion the fans have for the club and the level of expectation demanded from every player that pulls on the blue shirt.
“I have some fantastic memories of playing for Clitheroe Football Club and I look forward to making many more as manager.”
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