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Evidence suggests that children in low resource and humanitarian settings experienced added mental health burdens and violence in the home during the SARS-CoV-2 (COVID-19) pandemic, which may have affected their health and development. For humanitarian response agencies, conducting child protection services during this pandemic had been constrained by safety concerns related to the risk of COVID-19 transmission, and logistical issues aligned with social and public health measures. This paper describes how agencies responded to the identified risks children face, integrating remote risk communication and community engagement approaches and safe in-person dialogues with parents and caregivers into child protection interventions to educate about the disease and prevention, encourage a positive parenting environment and mitigate negative effects on children. United Nations (UN) agencies and non-government organizations (NGOs) must reflect on these different approaches and share lessons learned and best practices internally and at an inter-agency level to support evidence-based responses for future epidemics and pandemics.