Abstract Objective Salivary alpha amylase levels were measured to investigate sympathetic nervous system activity in migraine patients during attack, post-attack and interval periods of headache since salivary alpha amylase levels have been suggested as a potential indirect marker of sympatho-adrenal medullary activity in recent studies. Methods 50 patients with migraine headache (13 patients in attack, 26 patients in post-attack and 11 patients in interval period) and 60 healthy volunteers were taken into the study. In all participants, the presence of anxiety was measured by using Hamilton Anxiety Rating scale. The visual analog scale scores for pain level estimation were obtained in the attack group. Results The salivary alpha amylase levels were significantly lower in attack period ( p < 0.01) and higher in post-attack period ( p < 0.01) when compared with the control group. There was not any significant difference in salivary alpha amylase levels between interval period and control group ( p > 0.05). There was a weak negative correlation between the salivary alpha amylase levels and the visual analog scale scores. Conclusions This is the first study showing the dynamic nature of sympathetic nervous system activity by evaluating the salivary alpha amylase levels—a noninvasive, reliable and an easy method—in different periods of migraine headache.