How Migraines May Be Linked to Autoimmune Disorders
Last year, after dealing with months of unexplained fatigue and unpredictable migraines, I started wondering if something deeper was going on with my body. It wasn’t just the pain — it was the brain fog, the stiff joints, and the way even a small cold would knock me down for days. Eventually, I stumbled across the topic of autoimmune disorders, and I couldn’t help but ask myself: are migraines linked to autoimmune disorders? If you’ve been dealing with both or suspect a connection, you’re far from alone. Let’s talk through what the research, specialists, and personal experiences suggest.
Understanding the Basics: Migraines and Autoimmune Disorders
Before diving into their connection, it’s important to understand what each condition really is. Migraines aren’t just “bad headaches” — they’re a neurological condition involving sensory sensitivities, intense throbbing pain, nausea, and even temporary visual disturbances. Meanwhile, autoimmune disorders occur when the immune system mistakenly attacks the body’s own healthy tissue. Think lupus, multiple sclerosis, rheumatoid arthritis, and even celiac disease.
When I started seeing a neurologist who also had experience in autoimmune neurology, she mentioned that it’s not uncommon for patients with certain autoimmune diagnoses to also report chronic migraines. That got me curious enough to dig into the science — and there’s more overlap than I expected.
The central nervous system and immune system are more connected than we used to believe. In autoimmune diseases, the immune system creates inflammation throughout the body — including the brain. This inflammation can sensitize pain pathways and trigger migraine episodes, especially in people who already have a genetic predisposition to migraines.
Neuroinflammation as a Common Factor
Studies in journals like ncbi.nlm.nih.gov and sciencedirect.com have shown increased levels of pro-inflammatory cytokines in both migraine sufferers and people with autoimmune disorders. These inflammatory markers are known to disrupt the blood-brain barrier and amplify pain perception in the brain, especially in the trigeminal nerve — a common migraine hotspot.
Genetic Links and Family History
There’s a growing body of evidence that certain genes may influence the development of both migraines and autoimmune diseases. If autoimmune conditions run in your family, and you’ve struggled with frequent migraines since adolescence, it might not be a coincidence. My mother has lupus and I’ve battled migraines since I was a teen — go figure.
Common Autoimmune Conditions Linked to Migraines
- Lupus (SLE): Lupus patients often report recurring headaches that meet migraine criteria. Inflammation of blood vessels in the brain (vasculitis) may play a role.
- Multiple Sclerosis (MS): Migraines are more common in MS patients than in the general population. MS-related lesions in the brain may contribute.
- Rheumatoid Arthritis (RA): While not always neurologic, RA can cause widespread inflammation, indirectly increasing migraine risk.
- Celiac Disease: Gluten sensitivity in celiac patients may provoke immune-related migraines, often improving with a gluten-free diet.
Several people I’ve met through online support groups said their migraines decreased dramatically after they started managing their autoimmune disease more aggressively — especially through anti-inflammatory diets and medications like corticosteroids or DMARDs.
Triggering Factors That Overlap
Let’s talk triggers. Stress, hormonal fluctuations, poor sleep, and certain foods can spark both migraine flares and autoimmune flare-ups. That makes living with both conditions feel like walking a tightrope. You may want to check out our article on hormonal migraine triggers to get a deeper look into how these overlapping elements play out.
Personally, my biggest challenge has been sleep. I used to think sleeping more on the weekend would help. Spoiler alert: it didn’t. Consistency is everything — and sleep disorders themselves are a huge player in both autoimmune disorders and migraines, as detailed here: sleep disorders and migraines.
Getting the Right Diagnosis
If you suspect there’s a connection between your migraines and a possible autoimmune condition, don’t settle for vague answers. I bounced between doctors for over a year before I found a neurologist who took both concerns seriously. Tests for autoimmune antibodies, brain imaging, and even a migraine diary helped make the picture clearer.
- Keep a record of symptoms that seem to overlap.
- Track the timing of both migraine flares and other issues like joint pain, rashes, or extreme fatigue.
- Advocate for a full autoimmune workup if migraines don’t respond to standard treatments.
If you’re new to the migraine world, the main resource I’d recommend starting with is the Understanding Migraines article — it lays a great foundation for recognizing how complex and individualized this condition can be. For broader context, definitely refer to our main migraine and headaches guide to explore further topics as needed.
Managing Migraines When You Have an Autoimmune Disorder
If you’ve been officially diagnosed with both migraines and an autoimmune condition, managing them together can feel overwhelming. I’ve been there — juggling two different treatment plans, trying to figure out if it’s the inflammation talking or just a plain bad migraine day. It helps to approach the situation holistically, with patience and lots of self-trial and error.
Work With a Collaborative Care Team
This one made a huge difference for me. Instead of working with only a neurologist or just a rheumatologist, I found a practice that offered integrative care. A coordinated team approach made sure my migraine treatment didn’t accidentally flare my autoimmune condition — and vice versa. If you’re not sure where to start, our guide to finding a migraine specialist might point you in the right direction.
Anti-Inflammatory Lifestyle Adjustments
Some of the most noticeable improvements I experienced weren’t from medication — they came from consistent lifestyle tweaks that reduced inflammation. Here’s what worked best for me:
- Diet: Cutting out processed foods and focusing on omega-3s, leafy greens, and turmeric made a surprising difference. This guide on best foods for migraines offers great ideas that also align with autoimmune-safe diets.
- Hydration: Even mild dehydration triggered both joint stiffness and migraines. It’s an easy fix but often overlooked.
- Sleep: Getting 7–8 hours consistently (even on weekends) turned out to be one of the most powerful forms of prevention. More on this in our article on migraine sleep habits.
- Stress Reduction: Mindfulness apps, deep breathing, and yoga became my go-to strategies for stress — one of the top triggers for both conditions.
Medication Strategy: Less Is Often More
When it comes to medications, less sometimes really is more. Many autoimmune patients already take immune-modulating drugs, and adding a pile of migraine medications on top can quickly get messy. What helped me most was reviewing all meds with my pharmacist to check for potential interactions and duplications.
Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly used for both migraine and autoimmune flares — but they’re not a long-term solution and can affect your gut, kidneys, or liver if overused. I found some relief through prescription migraine medications that didn’t conflict with my autoimmune meds.
Other treatments worth looking into if you’re managing both conditions:
- CGRP inhibitors – specifically designed for migraine prevention with minimal immune suppression effects.
- Botox injections – safe for many autoimmune patients and can significantly reduce migraine frequency.
- CBT and biofeedback – effective, drug-free, and beneficial for emotional regulation.
Natural Remedies That Don’t Disrupt Autoimmune Balance
Trying natural approaches? That’s where I found the most trial and error. Not all “natural” treatments are safe for autoimmune diseases — for example, echinacea (often used for immunity) can actually overstimulate the immune system and worsen autoimmune symptoms.
Here are a few gentle, immune-friendly remedies that worked for me:
- Magnesium – helps with both migraine prevention and energy levels.
- Vitamin B2 and B6 – known for supporting nerve function and reducing migraine intensity.
- Essential oils – peppermint and lavender help me most during attacks, especially when combined with cold compresses.
Be Cautious With These
If you have autoimmune conditions, avoid anything that could spike your immune response. Some supplements, like ashwagandha or immune-boosting mushroom blends, can make things worse — always talk to your doctor first.
Monitoring and Tracking: The Underrated Game-Changer
I can’t stress enough how helpful it was to track both sets of symptoms. I used a digital migraine tracking app that let me log not just the headaches but also joint pain, skin rashes, GI symptoms, and even my mood. Patterns became much clearer — and so did the triggers.
One week I noticed I had migraines every time I ate tomatoes, but only during my autoimmune flare days. Turns out, nightshades were causing inflammation that led to both issues.
Living Fully With Both Conditions
Managing migraines when you have an autoimmune disorder is doable, but it takes self-awareness and a willingness to experiment. The good news is that treatments for both are improving — and support is out there. If you haven’t already, check out our comorbid conditions page to see how migraines overlap with other health issues, and our general guide on migraines and headaches to stay informed on new options.
Bianca Nala is a compassionate Nurse Practitioner with a strong background in primary and respiratory care. As a health writer for Healthusias.com, she combines her clinical expertise with a talent for clear, relatable storytelling to help readers better understand their health. Bianca focuses on topics like asthma, COPD, chronic cough, and overall lung health, aiming to simplify complex medical topics without losing accuracy. Whether she’s treating patients or writing articles, Bianca is driven by a single goal: making quality healthcare knowledge accessible to everyone.
