I visited the va for headaches, and was sent for a ct it came back with a cyst on right temporal lobe, told it wasn't the cause, can it cause headache?

Yes, arachnoid cyst: Arachnoid cysts are a congenital disorder -- most cases begin during infancy; however, onset may be delayed until adolescence. Headache, seizure, ataxia, nausea, are just some of the symptoms reported by patients. The next step is to see a neurologist to help manage your headaches. http://www.ninds.nih.gov/disorders/arachnoid_cysts/arachnoid_cysts.htm