The British filmmaker has previously helmed the acclaimed movies Kill List and A Field in England and will begin filming the episodes in December.
Wheatley: "I am very excited and honoured to be asked to direct the first two episodes of the new series of Doctor Who. I've been a fan since childhood (Tom Baker is my Doctor if you are asking). I've been watching the current run of Doctor Who with my son and have discovered it all over again. The work that has been done is amazing."
He added: "I'm really looking forward to working with Peter Capaldi and finding out where Steven Moffat is planning to take the new Doctor."