As first reported by Goal Australia, Miller departs the Jets after allegedly falling out with assistant coach Luc Trani during a recent pre-season trip to China.
Miller's time with the Jets was filled with frustration, culminating in an eighth-placed finish last season after taking over in June 2015.
Newcastle confirmed the departure in a statement, claiming the move was "based on differences related to football matters within the club."
"Newcastle Jets can confirm that the club has parted ways with head coach Scott Miller, effective immediately," the statement read.
"The club’s ownership and senior management made the decision on Wednesday morning. Since the decision was made Newcastle Jets chief executive officer Lawrie McKinna has met with Miller to discuss his departure from the club.
“We acknowledge that the timing of this decision is far from ideal given the proximity of next Hyundai A-League season,” McKinna said.
“But once the decision was made to move in a different direction regarding the head coach role we deemed it to be in everyone’s best interests to act quickly.
“I met with Scott this morning to inform him of the decision and discuss it.
“We thank Scott for the work he has done at the Club since being appointed by Football Federation Australia (FFA) last year and wish him well in his next position,” McKinna concluded.
McKinna has sought to notify all club players and staff today.
No time frame has yet been set for the appointment of a new coach at Newcastle.
The Jets have recently returned from China where they won all three of their pre-season matches.