Decide whether you want to create a traditional bedroom with "tribute" elements, a full-on fantasy setting bedroom, or a combination of both. With a traditional bedroom, plan to decorate with items like posters and printed bedsheets while otherwise retaining the conventions of a more or less ordinary room. If you're looking to create a fantasy setting, take the extended approach of transforming items in the room to look like life-size props and sets.
Browse catalogs of official "Doctor Who" merchandise to find bedroom accessories you can use in your design. Since "Doctor Who" is positioned as a family-friendly show, many toys and bedroom accessories are licensed through a wide variety of outlets. Look for merchandise through the BBC website or through your favorite toy sellers.
Adorn the floors, doors, windows and walls with "Doctor Who"-related textures and designs. For example, you might paint the door to look like the front of the TARDIS police box illusion, or paint the walls to look like those of your favorite version of the TARDIS interior (the fourth and 10th doctors' interiors are particularly distinctive). You might also paint the ceiling to look like a starry sky, swirling with the energies of a time vortex using glow-in-the-dark paint.
Brainstorm ways to give typical bedroom items a "Doctor Who" treatment. Consider things like a desk in the shape of a TARDIS console or a dresser shaped like a Dalek. Be creative elsewhere, imagining how a version of any given item might look like in the TARDIS. When in doubt, try a coat of metallic paint to tie items into a futuristic aesthetic.
Plan some means of prominently displaying classic "Doctor Who" prop replicas. No "Doctor Who" bedroom is complete without a sonic screwdriver (one of the easiest toys to find), but you might also try classic items like the fourth doctor's scarf, hung from a coat rack or the head of a Cyberman on a shelf.