The 66-year-old, who has been in the role since 2004, will leave York in 2015. It is not known why Mr Dyke, who was appointed the chairman of the FA during his tenure in 2013, will be leaving his position.
A spokesperson for the University said: “Greg will step down as Chancellor in 2015. He has done and continues to do an outstanding job for the University in this honorary position.”
The University will now consult with the Senate, Council Court and the student associations on a possible successor.
In accordance with the Charter, a final decision will be made by the University Court.
Mr Dyke previously hinted that he would have to leave his role in an interview with Vision last year after he was appointed the chairman of the FA.