The minister publicly disclosed his resignation at a press briefing
He said President Muhammadu Buhari accepted his resignation which he turned in a few weeks ago. The resignation is effective May 30.
Mr Fayemi emerged the candidate of the All Progressives Congress in the upcoming governorship elections in Ekiti on May 12.
The election is scheduled for July 14.
If Mr Fayemi wins, he would only be able to serve one term. He was denied a second term by Ayo Fayose in the state’s 2014 governorship elections.
He is expected to be the major challenger to the candidate of Peoples Democratic Party, Kolapo Olusola-Eleka, Mr Fayose’s preferred successor.