She has worked in the NHS for over 30 years and was appointed interim chief executive of the health board in January 2020 before being confirmed in the role that September.
In a statement, she said: “It has been a privilege to serve as chief executive of NHS Fife and to work alongside such talented and dedicated colleagues across health and social care.
“I am immensely proud of what we have achieved together, particularly in our response to the pandemic, our focus on continuous improvement and learning, and our shared commitment to delivering safe, effective, person-centred care for the people of Fife.”
Ms Potter will formally step down next summer and NHS Fife said arrangements will be made to appoint her successor.
Board chairwoman Pat Kilpatrick thanked Ms Potter for her “outstanding leadership” and contribution to NHS Fife and to the wider NHS in Scotland.
She said: “Her dedication to improving health services and outcomes for the people of Fife has been exemplary, and she leaves a strong legacy for her successor to build upon.”