Fishlock, 29, had been a player and assistant coach to Jo Montemurro, who has taken up a role with the club's men's team.
Her first match in charge will be the Round 11 fixture at Sydney FC on Sunday, 8 January.
Sydney are top of the table with Fishlock's side fourth.
Wales midfielder Jess Fishlock has taken over as Melbourne City coach for the final weeks of Australia's W-League season.