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WHO and the Collaborative Initiative for Paediatric HIV Education and Research (CIPHER) of the International AIDS Society (IAS) led a collaborative process to set global prioritized research agendas, aiming to focusing future research, funding, and stakeholder's efforts. This study describes the methodology used to establish the research agendas.The Child Health and Nutrition Research Initiative methodology was adapted in parallel exercises on pediatric and adolescent HIV. After definition of scope by an expert working group, priority questions were collected from stakeholders through an online survey. Submitted questions were coded, analyzed, and collated. The same respondents were asked to score the collated lists through a second online survey. The top 10 ranked questions per thematic area (testing, treatment, and service delivery) were reviewed and priority themes developed with consideration of existing policy, systematic reviews, and planned, ongoing, and recently published research.A total of 375 respondents submitted 1735 priority research questions. The majority of respondents were from Africa; 55% self-identified as researchers. The final collated lists included 51 and 61 research questions for pediatric and adolescent HIV, respectively. The response rate for the second survey was 48%. The final research agendas include 5 priority research themes per area, discussed in 2 separate publications.To date, this is the largest example of the Child Health and Nutrition Research Initiative method in pediatric and adolescent HIV in terms of stakeholders reached, and the first to incorporate top thematic areas based on current evidence. Its impact on improving outcomes for these populations will require strong political and financial commitment.