Migraines are known to be associated with EDS     

Headaches and migraines are very common with EDS, though the cause is varied. They can be due to TMJ Disorder, Chiari, Cranio-cervical Instability, POTS, Allergies, MCAS, Tension headaches, occipital nerve impingement because of lax necks, and many more causes. Seeing a headache specialist can be helpful to narrow down what type of headache or migraine it is, which may narrow down the cause. Of course, identifying the cause and addressing it is the best way to prevent the headaches or migraines if possible. See Dr. Lebron’s presentation slides from the 2014 EDNF Conference, “Ehlers-Danlos Syndrome and Headaches” http://ednf.org/sites/default/files/Diana%20Lebron.pdf

“Are headaches and migraine related to Ehlers-Danlos syndrome? Chronic recurrent headaches may constitute the neurologic presentation of EDS in the absence of structural, congenital or acquired CNS lesions that correlate with their symptoms. Individuals with EDS may be prone to migraine due to an inherent disorder of cerebrovascular reactivity or cortical excitability. Additional studies are needed to elucidate the pathogenesis of headaches in EDS. ”

[De Jacome. “Headache in EDS.” Cephalalgia 1999 Nov; 19 (9): 791.]
http://www.ednf.org/faq/are-headaches-and-migraine-related-ehlers-danlos-syndrome

As you can see, while there is agreement that migraines and other headaches are common in people with EDS, the reasons are not completely known.

There are headaches of a type called ‘cervicogenic headaches’ which means they are caused by problems in the neck, and this type of headache is also seen not uncommonly in EDS due to the many problems which EDSers can have in the area of the cervical spine. People with cranio cervical instability (CCI) or Chiari I malformation may also have headaches due to these conditions, which are associated with EDS as well.

(Acknowledgments: LorrieL and SASO on Inspire)