Background While the Global Burden of Disease (GBD) study reports headache disorders as the second-highest cause of disability worldwide, the headache data in GBD come very largely from adults. This national study in Lithuania was part of a global schools-based programme within the Global Campaign against Headache contributing data from children (7-11 years) and adolescents (12-17 years). Methods The methods followed the generic protocol for the global study. The basic study design was a cross-sectional survey. Self-completed structured questionnaires were administered, within classes, in 24 schools selected from seven regions of Lithuania to be nationally representative. Headache diagnostic questions were based on ICHD-3 beta criteria but for the inclusion of undifferentiated headache (UdH). Results Of 3714 potential participants, 2505 (children 1382 [55.2%], adolescents 1123 [44.8%]; males 1169 [46.7%], females 1336 [53.3%]) completed the questionnaire. Adolescents and males were therefore relatively under-represented, with non-participation (32.6%) due in most cases to lack of parental consent. Observed lifetime prevalence of headache was 92.2%. Gender- and age-adjusted 1-year prevalence was 76.6% (migraine: 21.4%; tension-type headache [TTH]: 25.6%; UdH: 24.0%; all headache on >= 15 days/month: 3.9%; probable medication-overuse headache: 0.8%). All headache types except UdH were more prevalent among females than males, and among adolescents than children. UdH showed a complex relationship with age, but represented 38.0% of all reported headache in children, 27.4% in adolescents. Headache yesterday (HY) was reported by 17.5%, almost double the 9.8% predicted from prevalence and headache frequency to have headache on any day. The reason was unclear. Conclusions Findings were not very different from those reported in Turkey and Austria, but with more TTH. Headache has, therefore, again been shown to be common in children and adolescents, and UdH confirmed as a headache type that must be recognised and included in accounts of headache in these age groups.