WAYS is being formed as a continuation of the successful satellite event ("International Forum of Young Scientists" or IFYS) of the UNESCO-ICSU World Conference on Science in 1999. Recognizing the new challenges of science at the beginning of the 21st century and problems that have to be faced by young scientists, the IFYS participants decided to establish an organization that would function as a forum to communicate the opinion of young scientists to decision-makers in science policy.

In 2001, at the UNESCO General Conference in Paris, general consensus was achieved about the opening of the IFYS Secretariat in Budapest. The decision was based on Hungary's long tradition of scientific and civil institutions comprising all generations of young scientists (from secondary school through undergraduate and postgraduate studies to postdoctoral level). These young scientist organisations provide a firm background for the creation of an international network.

In 2002, the IFYS Foundation was established by the Association of Hungarian Ph.D. Students. As a legal entity, the IFYS Foundation was charged with advocating on behalf of young scientists and securing financial support to further the mission of the organization.

A new name, World Academy of Young Scientists (WAYS), was also proposed. The acronym WAYS has multiple meanings: ways to access science, ways to encourage scientific cooperation among generations, ways to international scientific cooperation, ways to influence science policy, ways to eliminate barriers to scientific opportunity.

In 2003, due to the Trustee's effective lobby activity, the WAYS Secretariat was fully equipped and opened in Budapest (1 August 2003) with the support of UNESCO, the Hungarian National Commission for UNESCO, the Hungarian Ministry of Education and the Hungarian Academy of Sciences. The Secretariat, located in the Computer and Automation Research Institute of the Hungarian Academy of Sciences, is presently run by two full-time employees (Marta Maczel, Ph. D.; Maria Harsanyi).

Mr. Balint Magyar, Minister of Education of Hungary already reported on the establishment of the WAYS Secretariat in Budapest at the UNESCO General Conference on 3 October, 2003  in Paris.

WAYS made its debut at the World Science Forum, Budapest - 2003 with the participation of numerous young scientists and the organization of the session 'Forum of young scientists'