FA chairman David Bernstein has been defeated in his bid to stay in the role beyond the age limit of 70.
A proposal to allow him to stay on in the post beyond next May was rejected by the FA council.
The FA also failed to get through a proposal for board members to be paid a retainer and increased daily allowances - the proposal was withdrawn without a vote being taken.
Bernstein has proved himself someone not afraid to make a stand since he replaced Lord Triesman in December 2010.
He took the decision to strip John Terry of the England captaincy earlier this year, accepted the resignation of Fabio Capello as a result, and staged a lone and ultimately unsuccessful protest against the unopposed election of FIFA president Sepp Blatter.