Background: This study evaluated the health-related quality of life (HR-QoL) in patients with sagittal synostosis (SS), and the influence of frequent headaches and surgical techniques on the HR-QoL. Method: Patients with SS aged 8 to 18 years were invited to participate between June 2016 and February 2017. The Child Health Questionnaire was used to assess the HR-QoL. A detailed questionnaire was used to assess the severity of headache symptoms. The control group consisted of 353 school children aged 5 to 14 years. Results: In all, 95 parents of patients with SS were invited to participate, of whom 68 (71.6%) parents completed the CHQ-PF50. The mean age of the participating patients was 12.4 years (10.8 to 14.2). The Psychosocial- and Physical summary of the patients with SS was similar to the general population. In the distinct CHQ scales, “Family cohesion” (P=0.02) was higher, and “Mental health” (P=0.05) was lower compared with the general population. The type and timing of surgery did not affect the HR-QoL. Thirty-two patients (47.1%) reported having headache complaints at least once a month. The CHQ scores of SS patients with frequent headaches had a significantly lower score of mild to large effect than those without headaches. Conclusion: Patients with SS have a slightly lower to similar HR-QoL compared with the general population. In all, 47.1% of SS patients have frequent headaches, resulting in lower average HR-QoL. The type and timing of surgery did not affect the results. Clinicians should be aware of lower HR-QoL in some subgroups of patients with SS.