The UN refugee agency is governed by the UN General Assembly and the Economic and Social Council (ECOSOC). The agency's biennial programmes and the corresponding budget are approved by the UNHCR Executive Committee, currently composed of 85 members. The programmes and the budget are presented by the High Commissioner, currently António Guterres, who is appointed by the UN General Assembly. 

The mandate of UNHCR is defined by the 1950 UNHCR Statute. Originally, the UN refugee agency was established with a three-year mandate to assist the European refugees displaced by World War II. As displacement failed to disappear and has become a persistent problem over the years, the agency had to keep renewing its mandate every few years. Finally, in 2003 the UN General Assembly extended the organization's mandate for an indefinite period, "until the refugee problem is solved." 

As head of the organization, the High Commissioner is responsible for the direction and control of UNHCR. He or she directs the work of the agency with the assistance of a Deputy High Commissioner and Assistant High Commissioners for Protection and Operations. The High Commissioner reports annually to ECOSOC and the General Assembly on the work of UNHCR.

The agency has some 7,680 national and international staff working in more than 125 countries. Most of UNHCR’s operations are in the field where the agency’s core work is managed from a series of regional and country representations and offices, sub-offices and field offices, often in very remote locations. Operations in the countries are headed by Representatives of the High Commissioner. There are also a number of Regional Representatives who are responsible for the coordination of operations in a particular region like Central Europe, composed of a number of countries. 

Over the years, UNHCR’s worldwide operation has become highly complex, ranging from the recruitment of new staff and ensuring their security in dangerous situations to the procurement of everything from medical supplies and bulk food shipments to aircraft charters. Specific departments, mostly based in the Geneva Headquarters, oversee key areas, such as operations, protection, external relations, human resources and finances. A number of regional bureaux also liaise between headquarters and offices at the country level.