Highwood's exit comes just a fortnight after David Gallop announced he will finish up as chief executive officer at year's end.

FFA vice-chairman Heather Reid stepping away from her board duties as she battles cancer – in the wake of the controversy over her role in Alen Stajcic's dismissal – leaves just one woman, Kelly Barin Rosmarin, on the remaining board of five.

Highwood's resignation follows that of the only other woman on the FFA executive, company secretary Jo Setright, in April.

Women's Council chair Ros Moriarty is the only woman, and an outside chance at best, among the publicly speculated candidates - such as PFA chief John Didulica, Sydney FC boss Danny Townsend and Victorian chief Peter Filopoulos - tipped to step into Gallop's shoes.

Highwood, 38, leaves FFA after delivering the biggest sports registration database in Australia MyFootballClub, overseeing record participation growth in the sport and also the Aldi Miniroos program.

She kept a low profile during her tenure, especially during the ugly scenes around Stajcic's dismissal.

As head of women's football, it was Highwood who implemented the review process that eventually led Gallop and the FFA board to terminate Stajcic's reign and its subsequent shambolic handling.

However Highwood avoided the spotlight over the Stajcic row and insisted she was not responsible for the running of the Matildas, passing the buck to the FFA's head of high performance, Luke Casserly.

Stajcic was eventually paid out by FFA, apologised to by Reid for her comments on his exit, and hired as coach of Central Coast Mariners.

Both FFA and Stajcic have agreed not to comment further on the saga as part of a settlement.

“The anticipated restructure of the leagues presents the ideal time for me to leave FFA and to pursue new challenges and opportunities," said Highwood today.

"I’m both satisfied and proud of what has been accomplished in football development, at the grassroots and in women’s football during my time.

“I am proud of the outcomes we have been able to deliver in an often-complex stakeholder environment and with tight resources.

"There is a real opportunity now for the game to pull together and align under a new governance structure and I wish the FFA board and stakeholders all the best as they move into this new era for football.”

FFA CEO David Gallop paid tribute to Highwood's work and added: "Emma has been a champion for both women’s and community football in Australia.

"She has always demonstrated both a love for football and a desire to help it grow, develop and reach its potential.

"It’s not easy to manage participation in the largest participation sport in the country, but Emma was able to do so with great passion and innovation."