Background:  One of the symptoms of chronic kidney disease (CKD), especially in individuals receiving regular hemodialysis (HD), is headache. Objective: This study aims to describe the prevalence, characteristics, and consequences of headaches on children with CKD's quality of life as assessed by the Headache Impact Test-6 (HIT-6) score.  Methods: The CKD group (n = 50) and the HD group (n = 50) were included in this cross-sectional comparative analysis. The prevalence, characteristics, frequency, and severity of headaches were compared between the two patient groups. Results: The prevalence and frequency of headache were significantly higher in the HD group than in the CKD group with p-values: <0.001, 0.003 respectively. Patients with headache had significantly lower GFR and serum sodium (p-values: 0.002, 0.006) but higher serum phosphate and PTH (p-values: 0.035, 0.005) than those without headache. In HD patients, The HIT-6 score was found to have a statistically significant positive correlation with serum magnesium (p = 0.012, r = 0.412) and a statistically significant negative correlation with serum sodium (p = 0.006, r: -0.474). Conclusions: Headaches are more prevalent and more frequent in CKD children on HD than in those on conservative treatment. In HD patients, lower serum sodium and higher serum magnesium increase the headache severity based on the HIT-6 score.