In Jordan, refugee affairs are managed through a centralized, multi-level administrative structure, working closely with UNHCR and other international organisations.

At the central level, the Ministry of Interior (MoI) is the main authority for refugee entry, residency and security. It issues MoI service cards to Syrian refugees living outside camps, giving them access to public services such as healthcare and education. The Syrian Refugee Affairs Directorate (SRAD), under the MoI, manages the refugee camps. The Ministry of Planning and International Cooperation (MoPIC) coordinates the national refugee response and donor funding through the Jordan Response Plan. The Ministry of Justice oversees the administration of justice, including judicial processes involving refugees, while the Ministries of Labour, Education and Health regulate refugees' access to work permits, public schools and health services.

At the governorate level, governors under the MoI oversee security and the implementation of refugee policies in their regions, supported by the police. At the local level, municipalities provide basic services such as waste management and infrastructure in areas hosting large refugee populations, while camps such as Za'atari and Azraq are administered by SRAD in cooperation with UNHCR.

Although Jordan is not a party to the 1951 Refugee Convention, UNHCR registers refugees and issues documentation under a 1998 Memorandum of Understanding with the Government. UNHCR works with national authorities and NGOs on protection, legal aid, resettlement and humanitarian assistance.