Brian Butler, who was previously head of comms at the Home Office, will leave the BMA in October to start his own media training and crisis comms agency, Lines2take.
While at the BMA, Butler has been at the centre of intense disputes between the BMA and the Government over doctors' working hours.
In his previous role, he led Home Office comms during the 11 September 2001 attacks.
The BMA is actively looking for his replacement.
During his time at the Home Office, Butler set up the media emergency forums, which established rules of engagement between journalists and the emergency services in the event of a terrorist attack.
Butler said: ‘I have had a terrific time at the BMA, but I wanted a further challenge, as I am only 61. I am leaving to move in a new direction. I am concentrating on selling my voice and my crisis comms experience on 9/11 and 7/7.'
Butler's new agency will also offer film narration and scripting services, alongside quick-fire reviews of communications within an organisation.