The A-League's current chief Greg O'Rourke is set to retain his position at the helm of the competition as it transitions away from the control of Football Federation Australia.

The Herald understands O'Rourke - who has been FFA's head of A-League and W-League since the start of 2016 - is heavily favoured to lead the executive branch of the new organisation that will soon be set up to run Australia's professional leagues after Monday's historic independence agreement.

A-League head Greg O'Rourke is likely to retain his position when the competition is run independently of FFA. Credit:AAP

Despite constant friction between FFA and the clubs over the last few years, O'Rourke is well liked and respected by the owners and is seen as a safe pair of hands to steer the A-League, W-League and Y-League into a brave new era.

O'Rourke's appointment is not yet official - the new organisation does not even exist yet, and won't until the legalities of the separation are ironed out by the end of the month and then executed - but it's believed his suitability has been discussed informally amongst the clubs, who are all of a like mind.