Farquhar, who has served in the role for 23 years, plans to spend more time with his family, focus on philanthropy, and help the global technology industry.
The announcement came as Atlassian released its third-quarter results.
Farquhar will step down on August 31 and remain on the company’s board and assume a special advisor role.
“Mike will continue to lead as CEO as Atlassian pursues its mission to unleash the potential of every team and capitalize on its strengths in the AI era,” the company said in a statement.
Billionaires Farquhar and Cannon-Brookes are two of Australia’s richest entrepreneurs.
The Atlassian founders met at the University of New South Wales and financed their company with a $10,000 credit card debt
It grew to become a $79 billion enterprise with more than 300,000 customers globally.
“The contribution Scott has made in founding and building Atlassian is impossible to quantify,” said Cannon-Brookes.
Atlassian is now listed on the Nasdaq.