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The COVID-19 pandemic resulted in widespread school closures globally, including in Kenya. This educational disruption had potential adverse consequences for adolescent school learners including school dropout, learning loss, opportunity losses, loss of previously acquired skills, and loss of socio-emotional benefits of time spent with peers and teachers. This study was undertaken in four counties in Kenya—two urban (Nairobi, Kisumu) and two rural (Kilifi and Wajir). Focusing on adolescent girls aged 10–19, the study increased understanding of the impact of the COVID-19 pandemic on girls’ education outcomes to enable implementation of policies and programs to address immediate harms caused, and to be better prepared for future pandemics or crises that could lead to prolonged school closures. The study utilized quantitative and qualitative techniques used for previously established research studies of cohorts in Kenya. Between March and May 2022, 2,784 adolescents participated in phone interviews and 66 adolescents, as well as 46 parents and other adult stakeholders, participated in in-depth interviews. In addition, literacy, comprehension, and numeracy testing was undertaken with 658 of the adolescent respondents.