John Delaney is stepping aside the FAI effective immediately.
However the move is pending the completion of an independent investigation by the Association into issue of concern to the board.
John Delaney came under fire after it emerged that he had loaned the organisation 100,000 euro in 2017, and failed to answers questions about the loan at a Dail Committee.
Honorary Secretary Michael Cody and Honorary Treasurer Eddie Murray have both voluntarily resigning from the board.
Meanwhile Sport Ireland may consider requesting a full audit of the FAI if it's to restore funding to the Association.
It's appearing before the Oireachtas Sports Committee tomorrow, on which sits Kildare North Social Democrat TD, Catherine Murphy
Committee Chair Fergus O'Dowd says a forensic audit is badly needed.