The 'unbundling' of Australian football has finally been agreed after years of wrangling, and the newly formed Australian Professional Leagues has promised to save the struggling Newcastle Jets.

The APL will take over the running of the A-League, W-League, and Y-League from Football Australia after the deal was ratified at a board meeting on Thursday.

It means the clubs are now responsible for the marketing and commercialisation of the A-League.

A-League club owners have spent years fighting for independence from FA, with the spats turning ugly at times.

The owners feel independence will give them more power to grow their respective clubs and help strengthen the ailing competition.

The first big problem facing the APL is the Jets' perilous financial situation.

Jets owner Martin Lee has stopped putting money into the club and he is expected to be stripped of the licence.

A new owner is yet to be found, leaving Newcastle on shaky ground.

But APL chair and Western Sydney Wanderers owner Paul Lederer said the Jets would be saved.

"Newcastle is a very important area, a very sports-minded, very parochial (area). It's been a great area for us," Lederer said.

"And APL will step in and not let it go. It just can't happen. In one shape or another, Newcastle will have a team hopefully forever."

FA chief executive James Johnson said his organisation would also ensure the Jets' survival.

"The APL is not going to let them down, and neither will we," Johnson said.

"We're going to work together with APL to ensure we'll find a way to ensure the Newcastle Jets not only survive, but also thrive.

"We are quite a way down the path in finding an ownership model that will allow Newcastle Jets to continue this year.

"There are no risks at all that I see with Newcastle Jets not being in the league. I'm very confident we'll find a solution along with APL along these lines."

Under the new unbundling agreement, FA will still be responsible for items such as expansion, contraction, promotion and relegation, the AFC Champions League, FFA Cup, and all other domestic and international competitions.

Lederer described the deal as a historic moment that has generated a "euphoric feeling".

"The handbrake on the game is off; owners can finally invest in what they own and create value for the entire footballing ecosystem," he said.

The new model for the Professional Leagues will be implemented throughout the course of the 2020-21 A-League and W-League seasons.

The APL Board will comprise of five directors from the clubs, three independent directors, and one person appointed by Football Australia.

An independent chair, to be elected by the clubs and ratified by Football Australia, will have a casting vote on the APL Board.

Greg O'Rourke, currently Head of Leagues at Football Australia, will take on a new role as commissioner of the Professional Leagues for APL.