Fischer returned to Hungary in 1983 to found the Budapest Festival Orchestra (BFO), which initially was intended for a limited number of concerts a year on a part-time basis.

With the BFO, he has incorporated unorthodox ideas into practice, including allowing individual symphony musicians to contribute to concert programming, as in the "cocoa-concerts" for young children.

In April 2007, Fischer was named the principal conductor of the National Symphony Orchestra (Washington, D.C.), after Leonard Slatkin stepped down as music director in 2008.

He debuted in 2006 at Glyndebourne Festival Opera in a new production of Così fan tutte: In 2006, Fischer was named Principal Artist of the Orchestra of the Age of Enlightenment.

In October 2020, the Royal Concertgebouw Orchestra announced the appointment of Fischer as its next honorary guest conductor (honorair gastdirigent), effective with the 2021-2022 season.

His "Spinoza-Vertalingen" for soprano and chamber ensemble composed on a 17th-century Dutch translation of Baruch Spinoza's text has been performed in the Netherlands and Hungary.

His one-act opera The Red Heifer, "composed as a rebuke to what he and others see as growing tolerance for anti-Semitism in today's Hungary"[9] was premiered at the Millennium Hall, Budapest, in October 2013.

Other Philips recordings include works by Kodály, Dvořák and Fischer's own orchestration of Brahms's Hungarian Dances, which combine improvisations from Gypsy musicians with a symphony orchestra.

His recording of Mahler's Second Symphony with the Budapest Festival Orchestra for Channel Classics won a 2007 "Editor's Choice" Gramophone Award.

7, 8 & 9; excerpts from Wagner's Die Meistersingers and Götterdämmerung; Richard Strauss's Josephslegende; and a release of his own compositions including Spinoza translations and Eine Deutsch-Jiddische Kantate.

In response to COVID-19's impact, Fischer invented an acoustic face mask that featured plastic hands cupped around the wearer's ears.