Headache is one of the most common causes of presentation to the physician in children. We aimed to evaluate the dynamic thiol/disulfide homeostasis with a new method in children with headache and also to investigate the relationship between the headache type, pain severity and duration in our study. We included 40 patients diagnosed with migraine, 40 patients diagnosed with tension-type headache (TTH) and 40 healthy children in the study. No significant difference was found between the total thiol, native thiol, and disulfide levels of the patient and control groups. However, the disulfide/native thiol and disulfide/total thiol ratios were higher in the migraine group than in the TTH and control groups. No correlation was found between the Pediatric Migraine Disability Assessment (PedMIDAS) score and the headache duration and any of the thiol/disulfide parameters. A negative correlation was found between the total thiol and native thiol levels and the PedMIDAS score in the TTH group. Migraine and TTH patients have different effect to thiol/disulfide homeostasis.