SAIA was founded in 1990s at the Ministry of Education of the Slovak Republic. New political system naturally called for an independent information agency to guarantee access to information and provide advisory service on opportunities to study abroad. Such agency would also develop an open and transparent application system for distribution of scholarships offered to Slovak students and researchers by foreign governments and various non-profit organisations after the regime change.

SAIA registered as a civic association on the 1st January 1992 and later transformed itself into a non-profit organisation providing public-benefit services. Initially, the agency carried out its activities only in Bratislava and later started to open its regional offices in university towns. In 1993, SAIA was authorised by the Ministry of Education of SR to administer two new intergovernmental programmes: Action Austria – Slovakia, Co-operation in Science and Education and CEEPUS. After expanding its services to a new target group – non-governmental organisations – it became a service centre for the third sector. SAIA ceased its wide spectrum of activities in this area at the end of 2003.

Since 2004, SAIA has been working not only in the field of student and teacher mobility but it started to concentrate also on mobility of researchers from both public and private research organisations. It became a part of the European network of EURAXESS Service Centres, with funding from the European Commission and Ministry of Education.

As of 2006, SAIA started to implement two new programmes adopted by the Slovak Government and financed by the Ministry of Education – the M. R. Štefánik Fellowship Programme and the National Scholarship Programme for the Support of Mobility. The 1^st phase of the Štefánik Fellowship Programme ended in 2009 and after its renewal in 2011 the Ministry itself took care of selecting the scholarship holders. The National Scholarship Programme entered into the second phase of its implementation in 2011 and SAIA has again become its administrator on the base of public procurement results.

“NIL Fund Supporting Co-operation in the Field of Education” programme with funding from the EEA/Norwegian Financial Mechanisms and co-funding from the Slovak state budget, has been managed by SAIA from 2007 till the end of April 2011. At present (since 2014) SAIA administers a new programme financed by EEA Financial Mechanism and co-funded by the Slovak state budget - the EEA Scholarship Programme Slovakia.

At the beginning of 2010, the SciexNMS^ch (Swiss-Slovak Scholarship Fund) was launched in Slovakia, funded through the Swiss-Slovak Cooperation Programme in the Enlarged European Union. SAIA became the Coordination Unit for the programme.

Currently SAIA runs offices in five university towns (Bratislava, Banská Bystrica, Košice, Nitra, and Žilina) with 22 employees. Overall budget for scholarships and projects in all programmes totalls over € 2 million yearly, including operational and other programme costs. Within the respective programmes the selection of scholarship recipients and projects is done by independent gremia and committees, made up of representatives of Slovak universities, the Slovak Academy of Sciences, the Ministry of Education and other organisations from Slovakia and from abroad (e. g., embassies of other countries to Slovakia).