The BBC says Caroline Skinner “has decided to step down” from the role and will join BBC Drama Production in London.
Skinner joined the series after Moffat’s former co-Executive Producer’s Beth Willis and Piers Wenger left the show.
In a statement Skinner said: “It has been an honour to have been a part of Doctor Who, and a privilege to have worked with Steven Moffat and Matt Smith on this extraordinary show. I have hugely enjoyed my time in BBC Wales and would like to thank Faith Penhale, and our wonderful production team for their unending commitment and brilliance.”
Faith Penhale, Head of Drama BBC Wales, will take over as Executive Producer on an interim basis, and the BBC says a new appointment will be made ahead of the next series.
In a statement Penhale said: “I would like to take this opportunity to thank Caroline for her contribution to Doctor Who since taking on the role in 2011, on behalf of both the BBC and the show.
“She leaves the show in good shape – there’s a brilliant new series starting on Easter Saturday that will see the official arrival of the Doctor’s new companion! And the 50th Anniversary plans are on track to deliver audiences an unmissable event! I wish her all the very best for the future.”