The Council's Chief Executive Theo Leijser will leave the post at the end of this month.
The Authority said in a statement that Theo is departing after five years to "take his career in a new direction", having delivered "much of what he was appointed to do".
The statement follows this afternoon's Extraordinary Full Council meeting.
Theo is quoted as saying: “I am very sorry to be leaving the Isles of Scilly as I have thoroughly enjoyed my time living and working here. I have greatly valued working for the Council over the last five years. However, at this point in time this is the right move for me and my family.
“I believe that in partnership with Councillor colleagues, a great team of Officers, and external partners we have achieved a lot. I was set the task of bringing about change and transformation, and I believe I have done so. I have focused on achieving outcomes, transforming the way the Council works and creating a new narrative for the islands to meet the challenges facing Scilly. Smart Islands has put the Isles of Scilly on the map.
"I am very proud of what the Council has achieved over the past five years and am confident that both the Council and the Isles of Scilly are in a strong position to move forward.”
Council chairman Robert Francis said: “I would like to thank Theo for the work he has done over the past five years and wish him well. He leaves behind a strong and committed team of officers, staff and Councillors who will work together to build a bright future for the Isles of Scilly.
"I will be working with fellow Councillors to recruit Theo’s successor as soon as possible.”
Photo by Convergence Cornwall.