The STDF grew out of a joint communiqué issued by the Heads of FAO, OIE, World Bank, WHO and WTO at the Doha Ministerial Conference in November 2001. In the communiqué, the five organizations agreed to jointly explore new technical and financial mechanisms for coordination and resource mobilization to ensure the most effective use of technical and financial resources.

In August 2002, the five organizations started discussing the creation of a partnership and a trust fund, with seed funding from the World Bank and WTO. On 10 September 2004, they formally established the STDF through the adoption of a first Business Plan.  Membership of the STDF was further expanded in 2005 to include representatives of donors and developing countries. In 2007, observer status was granted to various organizations with SPS expertise or implementing SPS-related technical assistance projects.

Three independent evaluations of the STDF have been undertaken to date. The first one was completed in December 2005 (STDF-76) and led to the adoption of a Medium Term Strategy for the period 2007-2011. The second evaluation was completed in November 2008 (STDF-248). This evaluation judged STDF’s overall performance "to be good and in many important areas very good" and highlighted that STDF carries out an important role that no other organization would be able to accomplish. The third evaluation reviewed the period 2009-2013 (STDF-MTR). The report noted that “the results are impressive and a testament to the effective operation of the STDF”. Its role in coordinating assistance projects was also praised as “significant value added.” The performance of the Secretariat was rated as “efficient and cost effective”.