Alison Johnstone said the review will examine the number and position of women parliamentarians and their level of participation in the debating chamber.
She said it will take a broad look at any barriers to equal representation.
All of Holyrood’s parties will be represented in the board overseeing the audit.
A report making recommendations for improvement is due by the end of 2022.
The Presiding Officer said: “Last May’s election returned our most representative and diverse Parliament to date.
“We know, though, from viewing the Parliament’s make-up from 1999 until now that this welcome progress can’t be taken for granted.
“This is an important opportunity to have a broad look at how the Parliament takes account of barriers to equal representation in its work.
“Working with Holyrood’s political parties, parliamentary staff, pre-eminent academics and Engender, the audit will cover a wide range of issues.
“These will include the number and position of women parliamentarians, participation and intervention levels in chamber business and the impact of parliamentary procedures and policies.”
Professor Fiona Mackay of Edinburgh University is one of the academics advising the board.
She said: “When the Scottish Parliament was created in 1999, it was internationally praised for its world-leading levels of women’s representation and its attention to equal opportunities and participation.
“Now is a good time to take stock.
“This audit, based on a well-tested comparative framework, will let us know how well Scotland has done over the long haul.
“And, crucially, what work still needs to be done to make it an inclusive Parliament for the 21st century.”
Eilidh Dickson, policy and parliamentary manager at the feminist advocacy organisation Engender, said: “Women are under-represented in almost all areas of our democracy, resulting in policy decisions which not only ignore women, but actively deepen inequality.
“By examining the make-up of committees, gathering data on who is being invited to give evidence, and understanding where gender mainstreaming is being ignored, we can work towards a Scottish Parliament which can act as an exemplar for women’s equality.
“We are delighted to be involved in the project.”