Premier Jacinta Allan and Health Minister Mary-Anne Thomas announced the inquiry on Monday, after a fresh survey found two in five Victorian women live with chronic pain.
The inquiry will examine systemic issues, hear directly from women and be led by a panel of experts overseen by the Women's Health Advisory Council.
"For too long, women's health has been seen as a niche issue and it has not had the attention the support that it deserves," Ms Allan told reporters at parliament on Monday.
"There is a gender pain gap."
The government also released a survey of more than 1700 women into pain and their experiences with the health system.
The survey found about half of women reported period-related conditions affected their health and wellbeing and a third have health conditions that affect their ability to work and keep a job.
One in three women also reported insensitive and disrespectful health practitioners who left them feeling dismissed and unheard.
"Too many women are living with pain, pain that is often undiagnosed and untreated," Ms Thomas said.
"We want a health system that caters for all Victorians, that really meets the needs of all Victorians."
Submissions to the inquiry can be made from January 30, with women and gender diverse people welcome to share their stories.
There will then be a nine-week consultation period before the inquiry provides a report to government later this year.
The make-up of the inquiry's committee and terms of reference will be announced next week, Ms Thomas said.
"It's really important ... that we have this focused research in order to make sure we've got the best evidence available to support the health and wellbeing of the entire population," she said.
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