Anaemia among adolescents is a global health problem. However, evidence regarding its burden and risk factors, particularly for younger adolescents and in sub-Saharan Africa (SSA), remains scarce. We aimed to assess the prevalence and potential determinants of anaemia among urban and semi-urban in-school young adolescents in Ethiopia, Sudan and Tanzania. We conducted a school-based survey among 3558 adolescents aged 10-14 years. A capillary blood sample was used to assess haemoglobin concentration. We assessed anaemia prevalence and examined associations between measures at the individual, household and school levels and anaemia using Poisson regression models adjusted for school and country-level clustering. The prevalence of anaemia was 32.0% overall, and 10.8% in Ethiopia, 25.0% in Sudan and 58.3% in Tanzania. Being a boy [adjusted risk ratio (RR): 1.11, 95% confidence interval (CI): 1.08-1.15, p < 0.001], poorer diet quality (RR: 1.12, 95% CI: 1.02-1.23 p = 0.015), no school handwashing stations (RR: 1.26, 95% CI: 1.20-1.32, p < 0.001) and food insecurity (RR for moderate/severe anaemia: 1.06, 95% CI: 1.02-1.10, p = 0.002) were associated with increased anaemia risk. Younger age (RR: 0.91, 95% CI: 0.86-0.96, p < 0.001) and increasing height-for-age z-score (RR: 0.93, 95% CI: 0.91-0.95, p < 0.001) were associated with decreased anaemia risk. Associations were consistent for moderate or severe anaemia. There was no evidence of effect modification by sex. This study highlights anaemia as a public health problem and identified nutritional, dietary and hygiene measures as key risk factors of anaemia among young adolescents in SSA. School-based interventions addressing these factors could reduce the burden of anaemia in adolescence.