FFA chief executive David Gallop and chairman Chris Nikou made the announcement in Sydney a short time ago.
It’s understood an investigation by the FFA identified a poor culture under Stajcic’s watch.
The 45-year-old took on the role in 2014, overseeing the most successful period in the Matildas’ history.
His replacement is yet to be announced.
The women’s world cup gets underway in France in June.