In February 1990, Ján Budaj became the first chairman of the VPN (Public Against Violence) and in March of the same year he also became the vice-chairman of the then Slovak National Council (SNR), where, among other things, he initiated the establishment of the environmental committee. He led the VPN to the first free elections in June 1990 as the movement's chairman and leading candidate. On the last day of the elections, he withdrew from the candidate list due to accusations of alleged cooperation with the ŠtB. However, this information was not confirmed. In 2007, an official report was found in the archives of the Institute of National Memory, which proved that a secret collaborator named Ján Budaj was actually working against the regime.
In 1993, Budaj was a co-founder of the Alliance of Democrats of Slovakia (ADS). After merging with other parties, the Democratic Union (DÚ) was formed, which before the elections in 1998 became part of the Slovak Democratic Coalition (SDK). After the elections, he was a member of the National Council of the Slovak Republic (NRSR) for SDK until 2002. He also served as vice-chairman of the Committee for Culture and Media of the National Council of the Slovak Republic.
Ján Budaj, as chairman of the Zmena zdola party, ran for Igor Matovič's OĽaNO (Ordinary people and independent personalities) movement in 2016 and became a member of parliament.
In the parliamentary elections on February 29, 2020, he was a candidate for the grouping of parties and movements Ordinary People and Independent Personalities (OĽaNO), NOVA, Christian Union (KÚ) and Zmena zdola. He became a member of the National Council of the Slovak Republic (NR SR).
Ján Budaj was a member of the city council in Bratislava from 2006 to 2020 for the electoral district of Petržalka, and in 2013-2014 he also served as deputy mayor of Bratislava.
On March 21, 2020, President Zuzana Čaputová appointed Ján Budaj as Minister of the Environment in the government of Igor Matovič.