Can acid reflux cause headaches behind the eyes.?

Not likely: Although acid reflux can go up all the way to your sinuses, causing chronic irritation of the sinus lining and eustachian tube dysfunction, headache is not a common symptom of acid reflux. The more common manifestation of acid reflux that travels above the voice box is the feeling that there is always something "stuck" in the back of the throat.

Acid reflux headache: No acid reflux does not cause headache behind the eyes.