The side effects of carnitine are usually nausea and diarrhea. Headache is not usually listed as a side effect. It is important to make sure that the supplement is of good quality and that it is not contaminants that are causing the headache. One way to find out if the carnitine is the cause is to stop using it and see if the headaches go away. It may be possible to decrease the side effects by decreasing the dose and/or dividing the dose into several small doses throughout the day.