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Why do I experience headaches in the back of my head where my skull meets my neck when working out?

I am a 31 year old male without any history of headaches when exercising. I generally train in the evenings and I feel the pain about 10 to 15 minutes into my workout. If I push through the pain it generally subsides within 45 minutes, can this be due to training in a mostly fasted state ( I intermittent fast and my first meal is at 5pm a 240 cal 50g protein 4g carb 2.5g fat protein shake an hour before working out) I don't have problems when I train fasted in the morning.
That is a great question. There are a variety of reasons for pain in the back of the head that you are describing. These are some questions to consider as they may help elucidate what is the underlying cause for these headaches. Is the pain on one side or both? Does it radiate anywhere else (i.e. down the arms or legs)? Does the pain only occur when you are do exercises in the upper body (i.e. neck manipulation) or is it with all exercises? These are questions to think about and bring up with your primary care doctor because along with your medical history and presenting symptoms, he or she will better be able to decide upon the appropriate work up. This may include lab tests or imaging studies and perhaps a referral to a specialist. Based upon the description you have provided, some of the diagnoses that are more likely include dehydration, deficiencies in nutrients or vitamins, and overexertion of the muscles in your neck. Other less likely possibilities include occipital neuralgia or metabolic disorders. Some things to possibly treat the symptoms you are experiencing include muscle stretching, ice or warm packs, ensuring that you are well hydrated prior to working out.
This answer is for general informational purposes only and is not a substitute for professional medical advice.
If you think you may have a medical emergency, call your doctor or (in the United States) 911 immediately. Always seek the advice of your doctor before starting or changing treatment. Medical professionals who provide responses to health-related questions are intended third party beneficiaries with certain rights under Zocdoc’s Terms of Service.

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