Headaches have many causes and one of those causes is from the neck. These cervicogenic (neck originated) headaches start from the top of the neck and the base of the skull. Again- any headache that starts from these points may not from be from the neck. There are 2 nerves that exit out the back of the neck and go up behind the head and the ear. These are the greater and lesser occipital nerves. They can be aggravated by the facets (the joints) they lie next to. Also, there are rare occasions that the disc itself can refer pain to the back of the head.