Mr Williams will be succeeded by current deputy head of equities and portfolio manager Paul Skamvougeras, with Nathan Parkin stepping into the deputy head of equities role.
A statement released by Perpetual said that Mr Williams, who is 47 years old, has decided to "retire from Perpetual after 22 years".
In a media briefing held yesterday Perpetual chief executive Geoff Lloyd said the top priority over the next few months will be "managing the transition effectively".
The "immediate focus" for Mr Williams will be to ensure a "smooth transition from myself to Paul".
Mr Williams has employment restrictions in place and cannot join another fund manager until 16 July.
"So I've got plenty of time to think about whatever I may want to do," he said.
Reflecting on the decision to leave Perpetual, Mr Williams said he spoke to Mr Lloyd and Perpetual Investments group executive Michael Gordon before Christmas.
"We talked about the future and they told me to have a good think about it over the break. I did, and I’ve come back and the decision was made," Mr Williams said.
"There no simple answer to why, it’s just the right time. There’s a lot of factors that go into it. But after what will be 22 years I think the timing makes sense," he said.
*Correction: The original version of this article stated Matt Williams had left the Perpetual. This is incorrect. He will leave the company in September 2015 after overseeing his successor's transition.
