I believe so. I have migraines for years. I have taken klonopin for2 yrs now, and I experience migraines a lot more frequent. Hi, hope you are doing well, I do believe that it can cause headaches! As most meds have different affects on different people, most meds are going to have some kind of side affect as your body gets use to the med. What do you suggest if I have been on 2-3 mgs of klonopin (clonazepam) for over 10 years. Down to 2 mgs. Now tryi Down to 2 mgs. Now tryi more What do you suggest if I have been on 2-3 mgs of klonopin (clonazepam) for over 10 years. The klonopin is the same in all but the binders used are different in every generic and can effect patients in different ways. Hope this helps. Hope this helps. Jesse · 3 years ago Hello crispy63. Headaches are a side effect to taking Klonopin. Its considered to be a normal and common one. If it doesn't ease up, (usually this type of side effect will stop altogether the longer you remain on the drug) you might see your doctor and what your options could be. only upon withdrawal - approx. 36 hrs after last dose. Whether or not I'd taken klonopin once in a month or every day for a month. Also this is the only migraine I get that includes an aura. Clonazepam is the active ingredient in Klonopin, and can be referred to as “kpin” or “pin”. It is a benzodiazepine which means it acts as a sedative agent. 2 years ago my MD placed me on bid gabitrol 4mg and 1.0 mg Clonazepam for migraine prevention. Have had migraines since 13 yrs old and have tried various triptans, and tricylics. Doctors give unbiased, trusted information on whether Clonazepam can cause or treat Migraine: Dr. O'Malley on clonazepam for migraines: Xanax (alprazolam) is a very dangerous drug. It is highly addicting. Now I would avoid that drug and if you suffer from panic attacks there are safer choices of medication that have been approved for panic attacks Xanax (alprazolam) is not one of those.