Background: The Global Campaign against Headache collects data from children (6–11 years) and adolescents (12–17) to inform health and education policies and contribute to the Global Burden of Disease (GBD) study. This survey in Zambia, part of this global enquiry, was the second from sub-Saharan Africa (SSA). Methods: Following the generic protocol, this was a schools-based cross-sectional survey. We used the child and adolescent versions of the structured Headache-Attributed Restriction, Disability, Social Handicap and Impaired Participation (HARDSHIP) questionnaire, self-completed by pupils within classes, in a total of nine schools in Lusaka (urban) and Copperbelt (semi-rural). These two of Zambia’s ten provinces were selected to represent the country’s urban/rural divide. Headache diagnostic questions were based on ICHD-3 except for undifferentiated headache (UdH). Results: Of 2,759 potential participants, 2,089 (615 children [29.4%], 1,474 adolescents [70.6%]) completed questionnaires (participating proportion 75.7%). Children were therefore under-represented (mean age 13.1 ± 2.8 years), while gender distribution (1,128 [54.0%] male, 961 [46.0%] female) was close to expectation. Observed lifetime prevalence of headache was 97.5%. Gender- and age-adjusted 1-year prevalence estimates were 85.8% for all headache, 53.2% for migraine (definite 17.5%, probable 35.7%), 12.1% for tension-type headache (TTH), 14.8% for UdH, 3.3% for all headache on ≥ 15 days/month and 0.9% for probable medication-overuse headache. Headache durations were short: only 28.6% of participants with any headache, and only 10.5% of those diagnosed as probable migraine, reported usual durations of > 2 h (the threshold for definite migraine). Of the latter, 36.6% reported < 1 h, the duration criterion for UdH. There were weak associations of migraine (definite + probable) with female gender, and of TTH and headache on ≥ 15 days/month with adolescence. Headache yesterday was reported by 22.2% of the sample, 25.5% of those with headache. Conclusions: Headache disorders among young people are prevalent in Zambia. Among them, migraine is the most common, with UdH also highly prevalent. In this study there were diagnostic uncertainties, which rested to a large extent on the distinction between migraine and UdH among the many participants reporting headache of < 2 h’ duration. Similar uncertainties occurred in the first study in SSA, in Ethiopia. Because of these, we conclude only that migraine affects at least 17.5% of these age groups in Zambia, which is still a large proportion, adult prevalence in an earlier study being 22.9%. Supplementary estimates of attributed burden are needed to inform public-health and educational policies in Zambia.