The 40-second advert, which features new Doctor Matt Smith and assistant Karen Gillan, will be shown in cinemas nationwide before screenings of Alice In Wonderland.
The trailer is a converted version of the new 2D trailer that will premiere on BBC One this weekend.
A BBC spokesperson told Broadcast: "Doctor Who is the appropriate vehicle for 3D. It just fits. It’s a great way to introduce and showcase the new Doctor to younger viewers."
The new series of Who will launch in the Spring.