Can Allergies Cause Migraine Headaches? The Link Between Hormones, Histamine, and Head Pain

allergies headaches Mar 21, 2025

If you suffer from seasonal allergies and also experience migraine headaches, you may have wondered: Can allergies cause migraine headaches?

The short answer? Yes, allergies can contribute to headaches and migraines—especially for women with hormonal fluctuations. Understanding how allergens, histamine, and estrogen interact can help you better manage symptoms and prevent allergy-related headaches.

The Link Between Hormones & Allergies

Did you know that hormones influence how your body reacts to allergens? Research shows that estrogen, progesterone, and other hormones can impact the severity of allergic reactions, and in some cases, even trigger headaches and migraines.

If you’ve noticed that your headaches are worse during allergy season or at certain points in your cycle, your hormones could be playing a role.

Can Allergies Cause a Headache?

Yes—allergies can contribute to headaches in several ways. When pollen, dust, or mold enter the body, they trigger histamine release, which can lead to sinus pressure, inflammation, and headaches. High histamine levels can also affect the nervous system, leading to migraines in some individuals. Another major factor is the estrogen-histamine connection. Estrogen stimulates mast cells to release more histamine, which may worsen allergy symptoms and increase the risk of migraines. For women who already experience hormone-driven migraines, an allergy flare-up can act as a major trigger.

Sinus congestion from seasonal allergies is another culprit. When the sinuses become inflamed and swollen, it can cause pressure in the forehead, around the eyes, and in the temples—common areas where sinus headaches develop. Many people assume they have a regular migraine, but the underlying cause may actually be allergies.

Hormonal fluctuations also play a role in allergy-related headaches. Many women experience worsening headaches before their period, when estrogen levels drop. Since estrogen influences histamine levels, this can explain why allergy-related migraines feel more severe at certain times of the month. If you’ve been asking, “Can allergies cause migraine headaches?” the answer is yes, especially when histamine levels spike and hormonal changes occur simultaneously.

Estrogen & Allergies: Help or Harm?

Estrogen has a complex relationship with allergies and headaches. In some cases, it can make symptoms worse, while in others, it may actually help regulate the immune system. On one hand, estrogen can activate mast cells and eosinophils, triggering histamine release and inflammation. This may explain why some women experience worsening allergy symptoms and migraines during pregnancy, when estrogen levels are high. On the other hand, estrogen can also regulate immune responses and protect against airway inflammation, which may reduce allergy symptoms in some women.

Allergies, Headaches & the Menstrual Cycle

Your menstrual cycle plays a role in how allergies and headaches show up throughout the month. Many women notice that before their period, when estrogen levels drop, their allergy symptoms and migraines become worse. This is because estrogen plays a role in immune regulation, and when levels decrease, histamine can become more active, leading to increased inflammation and a higher likelihood of headaches.

Mid-cycle, when estrogen is at its peak during ovulation, some women actually experience relief from allergy symptoms. This is because estrogen enhances regulatory T cells, which help suppress allergic responses and inflammation. However, for those with histamine intolerance or sensitivity to estrogen surges, this phase may actually trigger headaches and allergy flare-ups.

In the second half of the cycle, as progesterone rises, some women notice nasal congestion and inflammation, which can contribute to sinus headaches. If progesterone levels are too low, estrogen remains relatively high, keeping histamine levels elevated and making allergy symptoms worse. If you’ve ever thought, “Could allergies cause migraines worse at certain times of the month?” your hormonal cycle could be the missing piece of the puzzle.

12 Natural Remedies for Allergies & Headaches

If you struggle with seasonal allergies and migraines, these natural remedies can help:

1. Keep Windows Closed

Pollen enters your home through open windows, worsening allergy symptoms and sinus headaches. Keep them shut—especially in the early morning and late afternoon when pollen counts are highest.

2. Use a High-Quality Air Purifier

A HEPA air purifier can filter out pollen, dust, and mold, helping to prevent allergy-related headaches.

3. Avoid Peak Pollen Hours

Try to stay indoors from 5 AM – 10 AM and in the late afternoon when pollen levels spike.

4. Use a Neti Pot

A neti pot or saline rinse can flush out allergens from your nasal passages, reducing inflammation, congestion, and sinus headaches.

5. Stay Hydrated

Drinking plenty of water, herbal teas, and broths helps thin mucus and flush out histamines that may trigger headaches and migraines.

6. Eat an Anti-Inflammatory Diet

Certain foods can help reduce allergy and headache symptoms naturally. Focus on:

Vitamin C-rich foods – Oranges, bell peppers, and berries help lower histamine levels.
Omega-3 fatty acids – Found in salmon, walnuts, and flaxseeds, these fight inflammation.
Leafy greens & colorful veggies – Support immune function and hormonal balance.

7. Avoid Dairy

Dairy increases mucus production and may worsen congestion and sinus headaches. Try limiting milk, cheese, and yogurt.

8. Support Gut Health with Probiotics

A healthy gut equals a strong immune system. Taking a daily probiotic or eating fermented foods like sauerkraut and non-dairy yogurt can regulate histamine responses.

9. Try Natural Antihistamines

Some natural compounds can help block histamine release and prevent allergy-related headaches:

Quercetin – Found in onions, apples, and green tea, acts as a natural antihistamine.
Bromelain – An enzyme from pineapple that reduces nasal swelling and inflammation.
Stinging Nettle – A powerful anti-inflammatory herb for allergy relief.

10. Reduce Inflammation with Turmeric & Ginger

Both turmeric and ginger contain anti-inflammatory properties that help calm immune overreactions and reduce histamine-driven headaches.

11. Hot/Cold Contrast Showers

Alternating between hot and cold water can improve circulation, relieve sinus pressure, and prevent headaches.

12. Keep Your Indoor Space Allergy-Free

Wash bedding in hot water weekly to kill dust mites and allergens.
Maintain indoor humidity at 30-50% to prevent mold growth.
Use a HEPA vacuum to trap allergens in carpets and upholstery.

Take Control of Your Allergies & Headaches This Season

If you suffer from seasonal allergies and migraines, understanding the hormone-histamine connection can help you predict and prevent symptoms more effectively. By reducing histamine exposure, supporting estrogen balance, and implementing natural allergy relief strategies, you can enjoy a clearer head and a healthier spring.

Need personalized support? Book a free discovery call to create a tailored plan for allergy relief and hormonal balance!