How do you know his ears are fine? There could be a problem deeper than you can see. You do need to be careful with the head shaking, that can cause an ear hematoma ... those are not pleasant and it can be very expensive.
I agree with Jo. Have it checked out..... could be a deep infection, foreign body, ruptured eardrum. And those hematomas often require surgery... not fun. Our old aussie, Syd, had this and now has one perky and one droopy ear.
Or, a hematoma starting could cause head shaking. They're little pockets of blood between the layers of the ear flap. This time of year foxtails or other grass seeds in the ears are quite common. Dogs ear canals have a bend in them, it's not easy to see all the way down.
Water in the ears too, or an infection. Lots of other less common reasons too. Vet check is always good for ears before things escalate.
My Ike was shaking his head from the time I brought him home from the Breeder. Every Vet check showed clear ears. The head shaking eventually caused trauma that led to infections in both ears. After recurrent infections and not getting a handle on things, we decided he had allergies, seasonal and food. I switched Ike to a corn, chicken, white rice, and soy free diet and give benadryl when I know that seasonal allergies are at their peak. This has worked for Ike. He went for a full year without an ear infection...though he's now being treated for one after getting into my daughter's dog's kibble while on vacation and has started the itching, scratching, and head shaking again.
Your pup might have seasonal or food allergies also. You might ask your Vet about Benadryl to ease the itching.