Headaches are the most common side effect associated with erectile dysfunction medications. Nitric oxide helps increase blood flow to the penis to create an erection, but this sudden change in blood flow can cause a headache.It is important to know that headaches are common with all forms of ED medications, so switching brands wonât necessarily alleviate such symptoms.itric oxide helps increase blood flow to the penis to create an erection, but this sudden change in blood flow can cause a headache. It is important to know that headaches are common with all forms of ED medications, so switching brands wonât necessarily alleviate such symptoms.