Can having parasites be one of the causes of migraine headache? At first guess I'd say it depends on what you eat, where you've been... where you've travelled to in the past, what kind of doctor you see, and how your body deals with foreign invaders.
Let's examine a little evidence... look at what to watch for and what natural treatments are available.
Can parasites cause headaches? Yes they can. They can also manifest depression, nausea, and neck stiffness. 
When I started studying nutrition twenty or so years ago, the scientific field and the natural therapy world were divided over what part the gut played with migraines. Now treating 'gut health' is mainstream medicine.
A healthy gut means effective and stable: digestion and absorption of food, serotonin production, intestinal microbiota, immune status, etc.
So, since your gut and your intestines are often the first points of cause for illness, it makes sense for it to be one of the the first things to consider to heal your body.
Parasites from raw food cause major digestion problems and are considered to be one of the causes of migraine headache by some doctors.
The raw or cooked food debate over enzymes and parasites has been going on for decades.
Like how many times have you heard that pregnant women should not eat sushi.
How do we know what to do, as lay men and women, to help reduce or eliminate our migraines if parasites are causing digestion problems and are one of the causes of migraine headache?
There has been very little research done to test the effectiveness of natural remedies and supplements on migraines alone, never mind the link between migraines and parasites.
But the studies that have been done all point to parasites being potential causes of migraine headache.  Dr. Michael Greger talks about pork parasites and toxoplasma which are found in meat... but they can also live in raw fruit and veg. 
It is very important, if you feel like you might have parasites in your stomach or intestines, to see your primary health care provider for a consultation, or to get a referral to a qualified nutritionist or naturopath.
The best way to test for a parasite is to get a stool test.
A functional medicine physician will do a comprehensive stool test.
Here are some signs to watch for:
Getting a proper diagnosis is fundamental so you can get the right treatment.
If you suspect this could be one of the causes of migraine headache for you, here are the best natural treatments for intestinal parasites that I know of:
Of course, it depends on what kind of parasite you get diagnosed with as to the treatment. One macrobiotic treatment would be to eat a teaspoon of raw brown rice every morning for 10 days. Three times a day is better. The raw rice has nothing for them to eat and grow from.
You can feel quite sick during the 'kill off' period. I sure did on many occasions, but it's a cheap and effective treatment.
For more serious cases, a course (or more) of antibiotics may be required.
Roundworms, tapeworms, pinworms, whipworms, and fluke are examples of worm parasites.
Because they come in so many different shapes and sizes, they can cause a very wide range of problems.
Some cause fever and inflammation, constipation or diarrhea. Some consume your food and starve you of much needed nutrition.
Paul Pitchford, author of Healing with Whole Foods: Asian Traditions and Modern Nutrition states that: the parasites and microbes that raw foods often harbor can ”weaken one’s center, making digestion and assimilation weak."
"This in turn reduces the body’s ability to build life-essence" or as the Chinese call it Jing.
Jing represents the body’s vital essence derived from "reproductive essences" that are necessary for growth and immunity and it affects the mind and the spirit.
Pitchford provides three ways to remove the parasites and
microbes from your raw vegetables using apple cider vinegar, hydrogen
peroxide, and Clorox™ Bleach (and only Clorox™ Bleach). Interestingly
he says that cabbage is the only raw vegetable that does not "infest humans" and that "in most areas of the world, raw salad is a rarity."
I am not sure if parasites are one of my causes of migraine headache, but I choose to wash all vegetables in ¼ cup of vinegar in a gallon of water before I eat them. Whether it is one of my causes of migraine headache or not, I’d rather be safe than sorry!
I won’t get right into the debate over raw or cooked foods as there are a huge number of points to cover and then consider. I will just pick out a few points as they pertain to my migraine diet recovery plan which is all pureed and cooked food. You can read about that here - Migraine Diet Recovery Plan: Methods and Portions.
The age old assumption exists that raw food is good and cooked food is bad. But there are pros and cons on both sides. Let's look at a few...
According to Jon Barron, author of Lessons of the Miracle Doctors, and
The Baseline of Health Foundation in his newsletter on enzymes and digestive health says that “processing and cooking destroy enzymes in food”.
He points out that "any sustained heat of approximately 118-129 degrees °F (48-54 °C) destroys virtually all enzymes." When we were young we could bounce back from the imbalances that this
caused, but as we age our lack of enzymes takes its toll.
Enzymes rich foods ”actually predigest in your stomach through the action of their own enzymes in a process called “autolytic” digestion. Before stomach acid enters the process, you can actually break down as much as 75% of your meal."
"Without that autolytic digestion” your body over compensates by producing too much stomach acid and added stress on the pancreas to produce large quantities of digestive enzymes in order to process the denatured proteins and food.
So Barron posits the idea that raw food has its own digestive
enzymes and that cooking or heating denatures proteins and enzymes.
Here are some quick points on the pros and cons of cooked food.
Barron cites an interesting study from the Journal of Agricultural and Food Chemistry regarding the effects of different cooking methods and its findings were that “water-cooking treatments better preserved the antioxidant compounds, particularly carotenoids, in all vegetables analyzed and ascorbic acid in carrots and courgettes. Steamed vegetables maintained a better texture quality than boiled ones, whereas boiled vegetables showed limited discoloration.”
My recovery plan uses the steaming as the only cooking method, so it is fabulous to see some research findings supporting it. The study concluded that each vegetable has a preferential cooking method "to preserve or improve its nutritional and physicochemical qualities."
One more pro: cooked food just takes less energy to digest and if you are recovering from a chronic illness or a really long migraine, then perhaps this is something for you to consider and experiment with. Especially if you suspect poor digestion to be one of your causes of migraine headache.
The exact causes of migraine headaches are still unknown. The current theory is that they are thought to be the result of abnormal brain activity temporarily affecting nerve signals, chemicals and blood vessels in our brain.
And although numerous treatments are available, it can still be trial and error to find what works for you - click here for more causes.
And you might like to check out the WebMD symptom checker available online here - WebMD symptom checker
Causes of Migraine Headache References:
1. Barron, Jon (2009) Digestive Enzymes - Raw Food Newsletter. [Online], Available at: http://www.jonbarron.org/enzymes/digestive-natural-health-newsletter-raw-food Accessed Feb. 24, 2012. Material originally published at www.jonbarron.org. Copyright © 1999-2011. Baseline of Health® Foundation. Used by permission of the Baseline of Health® Foundation. All rights reserved worldwide.
2. Barron, Jon (2003) Choosing Your Digestive Enzymes Newsletter. [Online], Available at: http://www.jonbarron.org/enzymes/natural-newsletter-digestive-health-part2 Accessed Feb. 24, 2012.
3. Pitchford, P. (2002) Healing with Whole Foods (3rd ed.). North Atlantic Books: Berkeley, CA. pp. 572 and 643.
4. Very Well Health (2018) Parasitic Infections of the Central Nervous System. Available [online] at: https://www.verywellhealth.com/parasitic-infections-of-the-central-nervous-system-2488670
5. Greger, M. M.D. (2014) Chronic Headaches & Pork Parasites. Available [online] at: https://nutritionfacts.org/2014/08/26/chronic-headaches-and-pork-parasites/ Accessed 20 Oct. 2018.
6. National Institutes of Health (2014) Recurrent headaches may be caused by cerebral toxoplasmosis. World Journal of Clinical Pediatrics. 2014 Aug 8; 3(3): 59–68. Published online 2014 Aug 8. at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4162438/