The minister tendered his resignation letter to the president three weeks ago.
Since Fayemi won the primary election on May 12, 2018, there's been public pressure on him to resign from President Muhammadu Buhari's cabinet to avoid a conflict of interest.
The gubernatorial candidate announced his resignation at a press briefing in Abuja on Wednesday, revealing that he tendered his resignation letter to the president three weeks ago.
During his press briefing, he said, "On one hand, I have a deep sense of pride about my contributions to the landmark achievements we have been able to achieve in the sector, and I am thus transitioning out with my head held high.
"On the other hand, I am overwhelmed by emotions as I bid goodbye to a sector that I, together with other patriots, have invested a great deal of passionate and patriotic efforts over the past two years.
"My sincere thanks and appreciation goes to His Excellency Mr. President and His Excellency the Vice President for the visionary leadership and prioritization of the sector; as well as to my ministerial colleague, Hon. Abubakar Bawa Bwari - Minister of State."
Fayemi was Ekiti state governor between 2010 and 2014 before he was defeated by Ayodele Fayose during his re-election attempt. He will now face Fayose's deputy, Prof. Kolapo Olusola, in the July 2018 election for a second crack at leading Ekiti for the second time.