Background: This research prioritization aimed to identify major research gaps in maternal, newborn, child and adolescent health (MNCAH) to help mitigate the direct and indirect effects of the COVID-19 pandemic. Methods: We adapted the Child Health and Nutrition Research Initiative methodology. We defined scope, domains, themes and scoring criteria. We approached diverse global experts via email to submit their research ideas in MNCAH and MNCAH-related cross-cutting/health systems area. We curated the research ideas as research questions (RQs) and sent them to the consenting experts for scoring via the online link. For each RQ, the research priority score (RPS) was calculated as an average of individual criterion scores and ranked based on RPS in each area. Results: We identified top-ranked 10 RQs in each maternal, newborn, and child and adolescent health and 5 in the cross-cutting/health systems area. In maternal health, indirect effects on care, measures to improve care, health risks and outcomes, and preventing and managing SARS-CoV-2 infection/COVID-19 disease were priority RQs. In newborn health, clinical characterization and managing SARS-CoV-2 infection/COVID-19 disease, mode of transmission and interventions to prevent transmission were the focus. For child and adolescent health, top-ranked RQs were indirect effects on care, clinical status and outcomes, interventions to protect against SARS-CoV-2 infection/COVID-19 disease, and educational institute-related RQs. The cross-cutting RQs were the effects of the pandemic on availability, access, care-seeking and utilization of MNCAH services and potential solutions. Conclusions: We call on partners, including governments, non-governmental organizations, research institutes, and donors, to address this urgent research agenda.