Whithouse has previously penned three Doctor Who episodes - School Reunion, The Vampires of Venice and The God Complex. He also wrote the Torchwood episode Greeks Bearing Gifts and is responsible for the hit BBC Three series Being Human.
At the SFX Weekender, the writer revealed that his story will is currently planned to form episode three of the 2012 series and will be one of the last to feature Karen Gillan as Amy and Arthur Darvill as Rory.
Meanwhile, Chris Chibnall's previous Doctor Who writing credits include 42 and the two-parter The Hungry Earth / Cold Blood. He also worked as a co-producer and writer on the first two series of Torchwood.
Mark Gatiss will also be contributing a script to the new thirteen-part run along with head writer and executive producer Steven Moffat.
Production on the next series of Doctor Who will begin in Cardiff on the 20th February and is expected to be broadcast on BBC One in the Autumn.
The news was revealed in the latest issue of Doctor Who Magazine which is on sale from tomorrow (Thursday 9 February).