Willis will leave the BBC at the end of this month, a couple of months before fellow executive producer Piers Wenger leaves the BBC to join Film 4.
The news means a new executive team will join showrunner Steven Moffat as the programme gears up for production on the 2012/2013 series of the show leading into the 50th anniversary year.
Willis has been an Executive Producer on the series for the past two years. She joined the series with Wenger at the same time as showrunner Steven Moffat, taking over for the arrival of Eleventh Doctor at the conclusion of The End of Time. Both have been responsible for 27 episodes of the Show.
Wills will leave the series at the end of this month with Wenger departing the BBC at the end of September. The BBC hopes to find a replacement for Willis in time for the filming of the Doctor Who Christmas special. It will then recruit a second executive producer before filming for the 33rd series begins.
Working with Steven Moffat, Piers Wenger and Matt Smith on the last two series of Doctor Who has been the most fantastic experience and I will miss them hugely... The plans taking shape for the next series of Doctor Who and for the 50th Anniversary are beyond exciting - and with Steven Moffat at the helm, this incredibly special time for the show is in very safe hands.
The BBC's Drama controller Ben Stephenson praised Willis for her work on Doctor Who.
Much of its current success is down to her vision and ambition for the show. She has been an inspiring and instrumental force and I know will be much missed by all of us, and especially Matt Smith and Steven Moffat.Steven Moffat added:
We couldn’t keep her forever, though God knows I tried. She is off to be brave and brilliant in brand new ways, and the sad news for Doctor Who is that it will be somewhere else.
Willis returns to Kudos where she produced the first two series of Ashes To Ashes. Chief executive of Kudos, Jane Featherstone, said
I’m chuffed to bits to be welcoming her back to Kudos, where her creative instincts and no-nonsense work ethic will make her a force to be reckoned with in the drama world.