Mr Taylor, who has been the CEO for the past four years and was previously in charge of the organisation's stadium operations division, oversaw the deal which handed control of Subiaco Oval to the government.
But his leadership has come under scrutiny in recent months after details of WAFC salaries were leaked to the media, sparking a parliamentary inquiry into the way in which the organisation spends its money.
“Gavin has made an outstanding contribution to WA football over his 10 years at the WAFC, including his last four and a half years as CEO," he said.
"He has carefully navigated WA football through the transition from Subiaco Oval, state funding negotiations, major industry reforms and more recently the COVID-19 pandemic. He will leave the role having re-cast our strategy and structure to ensure the foundations of the game are in great shape moving forward.”
Like most sporting organisations, the WAFC has been hit hard by the pandemic and several staff members have left the organisation, while others have worked only part time. It is understood there will be further departures in the coming weeks and months.
A WAFC committee, headed by Mr Martin, will be tasked with finding Mr Taylor's replacement.