Here’s What’s Actually Happening To Your Brain During A Migraine

If you get migraines, you already know they don’t just stay in your head. The pounding pain might be the headline symptom, but the real story is how an attack can throw your entire body out of whack — making light feel blinding, everyday sounds unbearable, and even simple texts impossible to answer.

That’s because a migraine isn’t just about sore neck muscles or scalp tension. It’s a full-body neurological event, driven by a cascade of changes in the brain. As nerve pathways fire differently and brain chemicals shift, the systems that control pain, mood, digestion, and sensory processing can all get pulled into the chaos at once.

“Comparing a migraine to a run-of-the-mill headache is like calling a tornado a ‘light wind.’” - Ramon Velazquez, Ph.D., neuroscientist and scientific advisor at Mind Lab Pro.

Experts now understand migraine as a complex neurological condition rooted in how the brain functions — not simply a stress headache or something you can push through with enough water and willpower. From subtle early warning signs like mood changes and fatigue to the post-migraine brain fog that can linger for hours (or days), an attack reflects a brain-wide shift.

Here’s what’s actually happening inside your brain during a migraine.

1. Migraines Begin With Activity In the Hypothalamus

Studies show that increased activation of the hypothalamus — a brain region that regulates crucial functions like body temperature, hunger, thirst, sleep-wake cycles, mood, heart rate, blood pressure, sex drive, and more — occurs as early as two days (or as late as a couple hours) prior to the onset of a migraine. Increased cerebral blood flow into the hypothalamus and the havoc it wreaks on the body’s homeostasis serves as a not-so-subtle sign that a migraine is on its way.

“The hypothalamus serves as an early warning system that is responsible for your pre-pain symptoms,” explains Dr. Maria Knöbel, M.D., Medical Director of Medical Cert UK. “This includes things such as sudden fatigue or intense food cravings.”

2. The Trigeminal Nerve Changes Your Brain Chemistry

While many people think migraines are just about head pain or changes in blood flow, the chemistry of the brain actually becomes altered, increasing inflammation and irritation throughout your meninges, or the protective layers of membrane that line your skull.

“During an attack, the trigeminal nerve releases neuropeptides including CGRP, substance P, and neurokinin A,” explains Erik Larson, PMHNP-BC, a psychiatric mental health nurse practitioner in Denver, Colorado. “These substances cause dural vasodilation and neurogenic inflammation.”

Dural vasodilation and neurogenic inflammation? Think pain and swelling, but inside your brain.

3. The Thalamus Spreads Pain Signals Throughout Your Brain

Once the hypothalamus is activated and the trigeminal nerve has increased inflammation and swelling in your brain, the thalamus becomes the messenger, spreading these heightened pain signals throughout your brain.

“The thalamus is basically leaving the door wide open for pain signals during the migraine event,” Knöbel says. “This explains why even the weight of your hair, or a soft touch can feel unbearable.”

4. Chemical Changes Inhibit Your Brain’s Natural Protective Instincts

During an attack, the balance of serotonin, dopamine, and other neurotransmitters — which normally inhibit or curb pain signals — is disrupted. So not only is pain being relayed throughout the brain, but it’s also poorly suppressed by the brain’s natural protective mechanisms.

The Aftermath: Temporary vs. Long-term Changes

“Comparing a migraine to a run-of-the-mill headache is like calling a tornado a ‘light wind,’” says Ramon Velazquez, Ph.D., a neuroscientist and scientific advisor at Mind Lab Pro. “A typical headache is localized and relatively mild. While we still think of a migraine as something that happens in the brain, it does engage the entire body.”

And while a migraine attack eventually passes, it doesn’t always leave without a trace. During an individual attack, changes in the brain that occur are reversible, and after the attack ends, your brain gradually returns to a baseline state. However, with frequent migraines, more persistent changes can develop over time.

“The sensitivity of pain pathways increases and the activation threshold for the trigeminal system decreases, making attacks more frequent,” Larson explains. “In some people, MRIs reveal small lesions in white matter, which typically do not lead to neurological deficits but indicate the long-term impact of the disease on the brain. Therefore, migraine is considered not an episodic pain, but a chronic neurobiological condition requiring a systemic approach to treatment."

Being Mindful Of Daily Habits

Dr. Rab Nawaz Khan, M.D., whose clinical practice includes acute stroke care, neurology, and neurorehabilitation, recommends individuals with migraines focus on consistency to avoid migraine triggers, and recommends having a plan for if and when a migraine attack does occur unexpectedly.

“[Regularity] means consistent sleep and wake times, regular meals with protein, and steady hydration,” Khan says. “Keep caffeine consistent and earlier in the day, because swings in caffeine intake can trigger attacks. Aim for 150 minutes per week of moderate exercise and add stress downshifting such as breathing practice or short walks, since stress is a common [migraine] trigger and also a common rebound trigger after stress ends.”

It’s important to talk to your doctor, neurologist, and/or therapist about what treatment options and combination of treatment options may work best for you.

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