Traveling to areas with higher counts of pollen, mold spores, dust mites, and animal allergens can impact your allergies. These allergens may also be present on a flight. This is from exposure to other people's clothing, shoes, hair, and luggage.
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Try antihistamines: For those with allergy symptoms and air pressure regulation difficulties, medications like Claritin, Zyrtec, or Allegra may be a good option. Antihistamines are often formulated to include decongestants (such as Claritin-D, Allegra-D, and Zyrtec-D).
Many pilots are unaware that there are wait times after each use of sedating antihistamines. For cetirizine (Zyrtec®) and levocetirizine (Xyzal®), you should not fly for 48 hours after taking the last dose. For diphenhydramine or doxylamine, you should not fly for 60 hours after taking the last dose.
The higher up you go, the thinner the atmosphere gets. That means breathing in the same amount of air gets you less oxygen than at a lower altitude. Altitude sickness happens when your body has trouble adjusting to the difference in how much oxygen you're getting with each breath.
When the plane changes elevation during descent and ascent the sinuses must equilibrate to match the air pressure in the cabin but when the sinuses and eustachian tubes are blocked equilibration can be an issue. The pain occurs because of the restriction of air flow causing pressure in our sinuses.