Immediately after graduation, Fischer joined the Federal Statistical Office. In 1990 he became its vice-chairman and held this position until the dissolution of Czechoslovakia, becoming the first vice-president of the newly established Czech Statistical Office. Since the beginning of the 1990s he led the team tallying the elections in the Czech Republic results. He appeared to be groomed to replace the long-time president Edvard Outrata who retired in August 1999; however the Social-Democratic government brought in an outsider Marie Bohatá from the academia. She fired Fischer in September 2000, whereupon he became Production Director of Taylor Nelson Sofres Factum. In 2001 he participated in an International Monetary Fund mission exploring possibilities of establishing a statistical bureau in East Timor. Since March 2002 he was a chief of research institutes at the Faculty of Informatics and Statistics of the University of Economics, Prague. After Bohatá resigned due to a scandal with a huge error in foreign trade balance, Fischer was appointed president of the Czech Statistical Office on 24 April 2003. He is a member of the Czech Statistical Society, the Scientific Council and Board of Trustees and a Scientific Board of the Jan Evangelista Purkyně University in Ústí nad Labem. Since April 2011, he is also a member of the board of Bruegel, the European think tank for international economics.
After the vote of no confidence of Mirek Topolánek's centre-right government in March 2009, in the middle of Czech Presidency of the European Union, Fischer was proposed to be the Prime Minister in April. He was nominated by Civic Democratic Party as independent. His government, nominated by both the Czech major parties was inaugurated on 8 May 2009 on the understanding that the early election would be in October; however unexpected development in the Constitutional Court and House of Deputies postponed them to May 2010. Fischer decided to remain in the government, where he proved very popular, until then although the parties offered him a post in the European Commission. He was a patron of the conference "Crimes of the Communist Regimes".
Candidate for President
In February 2012, Jan Fischer announced his candidacy for the presidential election of January 2013. He was, according to polls, the favourite of the election, along with former Prime Minister Miloš Zeman. However, he lost in the first round to Zeman and the Foreign Minister Karel Schwarzenberg. Prior to the election, he was criticised for his former membership in the Communist Party.