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.

Humberside Police said Daniel Hatfield, 52 and Matthew Higgins, 49, died "after suffering significant multiple injuries".
Their bodies were found at a house on May Street on Friday.
Two women, aged 27 and 36, and a 38-year-old man are being held in police custody.
Det Supt Matt Hutchinson said police were keen to find out more about the movements of the two men in the week before their deaths.
"We also want to speak to people who know anything about the murder or have information about people attending or leaving May Street in the week prior to the men being discovered," he said.
"It is important to re-iterate that these murders are being treated as an isolated incident, however high visibility patrols will continue in the area to provide additional reassure to the local community."

Police said the attacker was a 58-year-old white man armed with a handgun but did not release any further details.
Witnesses said the man opened fire about 20 minutes into a screening of a film at the Grand Theatre in Lafayette.
Hours earlier, US President Barack Obama told the BBC that gun law reform had been his "greatest frustration".
Police chief Jim Craft said officers responded to reports of a shooting at about 19:30 local time (00:30 GMT).
Mr Craft said nine people were taken to a local hospital with injuries ranging from critical to non-life-threatening.
The gunman's identity is known to police, Mr Craft added, but is not being released at this time.
"We don't know whether it was a random act, whether it was a domestic situation," Mr Craft said.
The police chief said that the gunman did have a criminal history but that it was "pretty old".
Dozens of emergency vehicles were dispatched to the scene of the shooting in Lafayette, a city of about 120,000 people.
One witness said she heard a loud bang like a firecracker and saw a man standing up and shooting during screening of the film Trainwreck.
"He wasn't saying anything. I didn't hear anybody screaming either," Katie Domingue told local newspaper The Advertiser.
About 100 people are thought to have been in the building at the time of the shooting.
Louisiana Governor Bobby Jindal, who arrived at the scene late on Thursday night, told reporters: "We will get through this. We are a resilient community."
"This is an awful night for Lafayette. This is an awful night for Louisiana. This is an awful night for the United States," he added.
US comedian and actress Amy Schumer, who stars in Trainwreck, tweeted: "My heart is broken and all my thoughts and prayers are with everyone in Louisiana."
The shooting comes as a jury deliberates the death penalty for a gunman who attacked a cinema in Colorado three years ago.
James Holmes, 27, killed 12 people and wounding 70 others in July 2012 at a screening of a Batman film near Denver.

The Scottish Fire and Rescue Service was alerted to the blaze in the ground floor flat in Alpha Drive at about midnight.
The 26-year-old was given oxygen at the scene.
The fire is understood to have broken out in the kitchen of the property.
Wales midfielder Jess Fishlock has taken over as Melbourne City coach for the final weeks of Australia's W-League season.
[NEXT_CONCEPT]
Three people have been arrested on suspicion of murder after the bodies of two men were found in the garden of a house in Hull.
[NEXT_CONCEPT]
A gunman has opened fire at a cinema in the US state of Louisiana, killing two people and injuring nine others before shooting himself, officials say.
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A man has been rescued from a fire in a flat in Glenrothes in Fife.