Fowler, 38, was appointed in February 2020 and departs after back-to-back defeats to Morpeth Town in the FA Cup and the league, where Radcliffe sit 20th with two wins from 12 games.
A club statement said: “Radcliffe FC confirm Manager Lee Fowler has left the club by mutual consent.
“All at Radcliffe Football Club would like to thank Lee for his considerable contribution to development at the club.
“A further statement will be issued in due course.”
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