Vaughan's resignation comes less than two weeks after the ARB Reform Group won a major election victory, securing five of the seven seats available on the board.
The group wants to drastically cut back the activities of the board and change the ARB's current stance on PI insurance and continuing professional development.
Vaughan, who steered the ARB ship for six turbulent years, will now become the director of professional standards at the Chartered Institute of Management Accountants (CIMA).
He said: 'I have enjoyed my time at the ARB. It has been challenging, but never the less rewarding.'
He added: 'I have been greatly supported by ARB's staff who, although small in number, are big on experience and knowledge.'
The end of Vaughan's tenure at the ARB did not come as a surprise to long-term board critic Ian Salisbury. He said: 'Robin Vaughan's timing is impeccable and I wish him every success in his new post.
'This clearly has been in the offing for some time and I trust that no move will be made on the appointment of his successor without consulting the newly elected members of the board.'
An announcement about the process of finding a new chief executive and registrar will be made 'in due course'.
Vaughan is understood to be taking up his new position at the CIMA on 24 April.