Rogers joined the club in January 2014 from Blackburn Rovers, becoming assistant manager to Matt Beard as the Reds won back-to-back Women’s Super League titles in 2013 and 2014.
Following Beard’s departure to Boston Breakers in 2015, he was installed as the new manager and guided the team for the past three years.
LFC chief executive officer Peter Moore said: “We would like to thank Scott for his contribution to Liverpool Ladies both as assistant manager and manager. He is a very talented manager who I am sure will have a very successful coaching career ahead of him.