We conducted a cross-sectional study among school/college students in Tanzania and Uganda to determine the prevalence of high blood pressure (BP) and associated factors. Participants were classified to have high BP if they had pre-hypertension or hypertension. Interviews were done using the WHO STEPS instrument. Using data from both countries (n = 1596), the overall prevalence of high BP was 40% (95% CI: 37-42). The prevalence of pre-hypertension was 29% (95% CI: 26-31) and that of hypertension was 11% (95% CI: 10-13). High BP was independently associated with obesity (aOR = 6.7, 95% CI: 2.2-20.0), male sex (aOR = 3.2, 95% CI: 2.4-4.4), and among males aged above 20 years (aOR = 5.5, 95% CI: 2.9-10.5). Consumption of fruits/vegetables was associated with decreased odds for high BP (aOR = 0.7, 95% CI: 0.50-0.98). The increasing burden of pre-hypertension across age groups could explain the early onset of hypertension and cardiovascular diseases (CVDs) among young African adults. There is a need for longitudinal studies to explore the drivers of pre-hypertension in East African adolescents.