Prior to 1998, Timor Aid was a Timorese and Australian activist organisation for the relief of Timor Leste under Indonesian occupation, known as the East Timor International Support Centre (ETISC). At that time, ETISC organised small welfare grants to orphanages, widows, disabled and the poor, and lobbied international decision makers for Timor Leste's cause.
In 1998, Timor Aid was officially registered as a charitable organisation with the Indonesian Ministry of Justice. The organisation begun direct aid work inside Timor Leste in September 1999 when the country's independence referendum resulted in the destruction of 80 per cent of the national infrastructure and the displacement of a third of the Timorese population. In association with the Australian Foundation for the Peoples of Asia and the Pacific (AFAP), Timor Aid mounted a large emergency relief initiative, providing desperately needed food, medical supplies, shelter and clothing, with funding from the United Nations High Commission for Refugees (UNHCR), the World Food Program (WFP), the UK Department for International Development (DfID) and USAID.
Timor Aid's first long term development projects started in December 1999 with the opening of a sewing and weaving workshop in Dili, establishment of the women's development program funded by the European Commission (EC), and the establishment of the East Timor Vocational Training Centre in partnership with the local United Nations Development Program (UNDP) ofice. Since then, Timor Aid has grown into one of the largest Timorese non government organisations and has implemented around 100 small and large development projects including major projects funded by a number of European Governments, the European Commission, USAID, AusAid and United Nations agencies.