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Could be mites, some kind of ear infection, maybe something caught in throat that isn't passing down to the crop. If it's throat or ear mites, I'd suggest a few drops of Ivermectin orally and a single drop in each ear. If that stops the head shaking, you'll know it probably was mites.
Subsequently, one may also ask, why do my chickens shake their heads?
Heavenly Grains for Hens Try talking to them and see if they do it. Also this can happen with mites as others said, where they shake their heads every 5-15 seconds- I have seen that before. Additionally respiratory disease, ear mites, ear infection, etc. can cause it.
Then, why do chickens shake their heads when you talk to them?
I raised parrots for many years before getting into chickens and I know that parrots shake their heads when you speak to them because it's how they recognize and acknowledge that not only are you speaking to them, but that they recognize your voice, and your tonal inflection.
Chickens don't get ear mites. Dogs, cats, and humans can get bird mites however. They can't reproduce on mammals, so the infestation is short-lived, but can be very itchy.