SH5,
The strap muscles of the neck, especially the sternocleidomastoid muscle (SCM), are frequently injured in motor vehicle accidents.
The SCM goes from the clavicle in the front, up the side of the nec, and attaches to the middle or back of the head. So this could be it.
But, some people get a hot poker type fealing on the back of the head, going down the back of the neck, from tweeking the occiptal nerve (one of the upper C spine nerves). These are usually very fleeting, but could persist.
If it is really bothering you, you should see a physician about it. Good luck.