Headaches stem from a range of causes- two of the most common reasons are tight muscles and poor hydration. "The trapezius attaches high on your scalp, so if you hold a lot of tension in your upper body as you run, your head could ache. Headaches are also a symptom of both under-drinking and over-drinking.
Solution: Shake out your arms and hands and move your neck side to side occasionally as you run. At home, hold your left ear toward your left shoulder, right toward your right; repeat with the chin. Make sure you are hydrating just right; typically most people are dehydrated instead of over-hydrated.