Background: We previously reported high prevalences of headache disorders among children (6–11 years) and adolescents (12–17 years) in Ethiopia. Here we provide data on headache-attributed burden collected contemporaneously from the same study participants. Part of the global schools-based programme within the Global Campaign against Headache, the study is the first to present such data from sub-Saharan Africa. Methods: A cross-sectional survey following the generic protocol for the global study was conducted in six schools (urban and rural), in Addis Ababa city and three regions of Ethiopia. The child or adolescent versions of the Headache-Attributed Restriction, Disability, Social Handicap and Impaired Participation (HARDSHIP) structured questionnaires were self-completed under supervision by pupils in class. Headache diagnostic questions were based on ICHD-3 beta but for the inclusion of undifferentiated headache (UdH). Results: Of 2,349 eligible participants, 2,344 completed the questionnaires (1,011 children [43.1%], 1,333 adolescents [56.9%]; 1,157 males [49.4%], 1,187 females [50.6%]; participating proportion 99.8%). Gender- and age-adjusted 1-year prevalence of headache, reported previously, was 72.8% (migraine: 38.6%; tension-type headache [TTH]: 19.9%; UdH: 12.3%; headache on ≥ 15 days/month (H15+): 1.2%). Mean headache frequency was 2.6 days/4 weeks but, with mean duration of 2.7 h, mean proportion of time with headache was only 1.0% (migraine: 1.4%; TTH: 0.7%; H15+: 9.1%). Mean intensity was 1.8 on a scale of 1–3. Symptomatic medication was consumed on about one third of headache days across headache types. Lost school time reportedly averaged 0.7 days over the preceding 4 weeks, representing 3.5% of school time, but was 2.4 days/4 weeks (12.0%) in the important small minority with H15+. However, actual absences with headache the day before indicated averages overall of 9.7% of school time lost, and 13.3% among those with migraine. Emotional impact and quality-of-life scores reflected other measures of burden, with clear adverse impact gradients (H15 + > migraine > TTH > UdH). Conclusions: The high prevalence of headache among children and adolescents in Ethiopia, who represent half its population, is associated with substantial burden. Lost school time is probably the most important consequence. Estimates suggest a quite deleterious effect, likely to be reflected in both individual prospects and the prosperity of society.