A headache can be frustrating on its own, but figuring out why your head hurts can be even more difficult. During flu and allergy season, a headache may be caused by several different things. The flu and seasonal allergies can both cause congestion, fatigue, and pressure around the head and face. However, they usually come with different combinations of symptoms. Looking at the bigger picture, including whether you have a fever, body aches, itchy eyes ...