Background. Following disasters, separated and unaccompanied children are among the most vulnerable, therefore international organisations have formed guidelines regarding the management of these children. Guidelines include recommendations for identifying and registering children, tracing family members, reunification and arrangements for interim and durable care. There is a lack of experiential evidence on how these principles are put into practice at operational levels, and whether existing policies were useful. There is a particular lack of empirical evidence from the disaster prone country of Iran. The aim of this study was to describe the role of Non- Governmental Organisations (NGOs) in the management of separated and unaccompanied children, following disasters in Iran in order to plan for and provision of future disasters. Findings. The Iranian Red Crescent Organisation, Committee Emdad Imam Khomeini (a national organisation unique to Iran that is protected by the government and supported by public contributions) and Behzisti (the government welfare organisation in Iran) are the main figures involved in the management of separated and unaccompanied children, following disasters in Iran. NGOs are rarely responsible for caring for unaccompanied children, however they provide valuable support including financial assistance, arrangement of educational and extra-curricular activities and psychosocial support. Following the initial chaos after the Bam earthquake, international guidelines on separated and unaccompanied children were largely followed. Conclusions. Systems for managing separated and unaccompanied children following disasters in Iran, involving NGOs, are emerging. However, most are yet to be formalised.