After it stripped Nathan Tinkler of his A-League licence last week and taking control of the embattled club, FFA decided to punt Stubbins and his support staff after a review of the Jets' performance 'in relation to Hyundai A-League benchmarks for technical, tactical, conditioning and sports science'.
"Clearly, the Jets had a difficult season and this was reflected in the position on the A-League table," Head of A-League Damien de Bohun was quoted saying in an FFA statement.
"But this decision is also driven by the desire in the Newcastle football community for a new beginning with the new club."
FFA will allow the newly appointed coach to select his coaching team - meaning Stubbins' assistant coaches Mark Jones and James Pascoe, and goalkeeper coach Jess Vanstrattan, will nt be retained.
"Phil is a decent football man and we wish him all the best with the next stage of his career," De Bohun added.
Under Stubbins last season, the Jets finished last with a host of senior players shown the door in acromonious circumstances.
FFA declared last week that all 15 players contracted to the Jets would be offered new deals with defender Nigel Boogard the big-name off-season recruit from Adelaide United.