Background To investigate the effectiveness of chiropractic spinal manipulation versus sham manipulation in children aged 7-14 with recurrent headaches.Methods Design: A two-arm, single-blind, superiority randomised controlled trial.Setting: One chiropractic clinic and one paediatric specialty practice in Denmark Participants: 199 children aged 7 to 14 years, who experienced at least one episode of headache per week for the previous 6 months and with at least one musculoskeletal dysfunction identified. Interventions: All participants and parents received standard oral and written advice to reduce headaches. In addition, children in the active treatment group received chiropractic spinal manipulation and children in the control group received sham manipulation for a period of 4 months. Number and frequency of treatments were based on the chiropractor’s individual evaluation in the active treatment group, and the children in the control group received approximately eight visits during the treatment period.Primary outcome measures: ‘Number of days with headache’, ‘pain intensity’ and ‘medication’ were reported weekly by text messages, and global perceived effect by text message after 4 months. A planned fixed sequence strategy based on an initial outcome data analysis was used to prioritize outcomes. ‘Number of days with headache’ and ‘pain intensity’ were chosen as equally important outcomes of highest priority, followed by global perceived effect and medication. The significance level for the first two outcomes was fixed to 0.025 to take multiplicity into account.Results Chiropractic spinal manipulation resulted in significantly fewer days with headaches (reduction of 0.81 vs. 0.41, p=0.019, NNT=7 for 20% improvement) and better global perceived effect (dichotomized into improved/not improved, OR=2.8 (95% CI: 1.5-5.3), NNT=5) compared with a sham manipulation procedure. There was no difference between groups for pain intensity during headache episodes. Due to methodological shortcomings, no conclusions could be drawn about medication use.Conclusions Chiropractic spinal manipulation resulted in fewer headaches and higher global perceived effect, with only minor side effects. It did not lower the intensity of the headaches.Since the treatment is easily applicable, of low cost and minor side effects, chiropractic spinal manipulation might be considered as a valuable treatment option for children with recurrent headaches.Trial registration ClinicalTrials.gov, identifier NCT02684916, registered 02/18/2016 – retrospectively registered. https://clinicaltrials.gov/ct2/show/NCT02684916