Pitt-Brooke is director-general of media and communications in charge of around 130 comms staff.
The MoD has already started hunting a replacement for what is one of the most high-pressure comms jobs in government.
Issues Pitt-Brooke has faced in the role include media scrutiny over allegations of abuse at domestic bases as well as those in war-torn Iraq.
Responsibilities include overseeing the MoD’s entire news operation, which continues to be run by director of news James Clark.
The position also has ultimate responsibility for the Army’s planning and strategy desk, headed by Nick Gurr, and defence PR – which takes in non-news media items – overseen by Mark Lloyd.
The Whitehall central press office, seven regional press offices and The Defence Media Operations Centre and Joint Media Operations Team (JMOT) – which are deployed to the field with journalists and VIP guests – also report to Pitt-Brooke.
The role is traditionally filled by mainstream civil servants rather than lifelong comms specialists.
Pitt-Brooke, who was unavailable for comment, has worked for the MoD for over 30 years. A date for his exit has not yet been set.