Ms Ratchanee entered the board meeting room and declared her decision to step down from the board before walking out of the room.
The meeting took place as MRTA union members - most of them in black - held a rally in front of the room demanding all board members resign to clear seats so that the National Council for Peace and Order can revamp the agency.
Ms Ratchanee told the union representatives of her decision and showed her resignation letter before quickly leaving.
The meeting was adjourned after her shock announcement.
MRTA governor Yongsit Rojsrikul said her decision will be forwarded to the Transport Ministry, which oversees the agency. The MRTA will ask lawyers to study whether the resignation would mean the end of other board members' tensures.
At least it will delay a bid for the Green Line which is four months behind schedule, he added.
The bid will be called after a new board chair is appointed, he said.
The Green Line will be constructed from Mor Chit to Saphan Mai and Ku Kot.