Mark Batho, who has led the SFC since 2008, will in September take up the role of vice-principal for university services at the University of Abertay Dundee.
Last month it was announced that Sir Alan Langlands, the chief executive of the Higher Education Funding Council for England, will become vice-chancellor of the University of Leeds this October.
In a statement, the SFC’s chair, John McClelland, said: “Mark has led SFC through two periods of significant change and has ensured the council’s continued delivery against the organisation’s and the Scottish government’s priorities.”
Mr Batho said: “I am privileged to be joining Abertay university at this time, I am already familiar with the university and its ambitions for the future and I am very much looking forward to joining the team that will make those ambitions a reality.”
During his time at the helm, the SFC sent a letter in September 2011 suggesting that Abertay and the University of Dundee discuss the possibility of merging.
However following a hostile reaction from both universities, the merger agenda appears to have disappeared.
The university said Mr Batho would be responsible for its “strategic planning and resource allocation” as well as its support services.
In the summer of 2011 Abertay was rocked by the acrimonious departure of its former principal Bernard King, who refused to accept a statement from the university saying that he had retired.
The two parties later resolved their issues and withdrew legal claims against each other, although the true reason for Professor King’s departure remains a mystery.