The Swedish Committee for Afghanistan Board bears overall responsibility for all operations in Sweden and in Afghanistan. The Board is appointed at the SCA annual general meeting.

The SCA Secretary-General, Andreas Stefansson, leads operations and reports to the Board.

In Sweden there is an office of around twenty employees, working with fundraising, communications, aid coordination, and administration.

The majority of operations are carried out in Afghanistan, where the organization has more than 6,000 employees. Afghan headquarters are in Kabul. Operations are then divided among five regional offices who lead local activities.