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There are several reasons someone may waken with a headache. Migraine can certainly occur during the night. Sometimes neck problems can cause people to waken with a headache, and some find relief with special pillows. Sleep apnea is a condition where people do not breathe properly at night. People with sleep apnea may snore excessively, and a headache upon awakening is a common symptom. A variety of brain disorders may also cause headaches that are present upon arising, and this should be evaluated by your doctor. If a cause is not found, then a preventative medication taken at bedtime might be effective.Helpful? 2 people found this helpful.