Franz Fischler's career as a representative of the agriculture sector began in 1979 when he joined the Provincial Chamber of Agriculture of Tyrol. He dealt with environmental issues, education and training, culture and land-use planning until 1984, when he became Director of the Chamber. In 1989, he was appointed Federal Minister of Agriculture and Forestry in Austria. In that capacity he played an important part in the negotiations for Austria's accession to the European Union. From 1995 to 1999 he was European Commissioner for Agriculture and Rural Development and from September 1999 until 2004, he was also responsible for Community fisheries policy. From 2012 to 2015, Franz Fischler became the Chairman of the RISE-Foundation in Brussels. Furthermore, in 2014/2015 he was the Chairman of the Steering Committee of the EU scientific programme for Expo Milano 2015 as well as from December 2015, he has been President of the Board of Trustees to the Austrian Institute of Advanced Studies (IHS).

Since December 2004, Franz Fischler is concentrating on doing consultancy work, giving lectures, holding speeches and fulfilling his tasks being President of the think tank “European Forum Alpbach” since 2012.