As well as his solo work as flautist in the baroque repertoire, Brüggen also co-founded the Orchestra of the 18th Century which specialises in early music played on authentic instruments or copies of them.

Brüggen also conducted many leading European orchestras, including the Royal Concertgebouw Orchestra, and was a visiting professor at Harvard University.

Born in Amsterdam, Brüggen studied recorder and flute at the Conservatorium van Amsterdam. He also studied musicology at the University of Amsterdam. In 1955, at the age of 21, he was appointed professor at the Royal Conservatory of The Hague. Brüggen has been a visiting professor at Harvard University and the University of California, Berkeley.

In addition to his career as a soloist in the baroque repertoire, Brüggen co-founded the Orchestra of the 18th Century (Orkest van de Achttiende Eeuw) in 1981, along with Sieuwert Verster. He conducted many leading European orchestras, including the Royal Concertgebouw Orchestra. He was the conductor of the Radio Kamerorkest from 1991 to 1994, and joint chief conductor of the orchestra, alongside Peter Eötvös, from 2001 until the dissolution of the orchestra in 2005. He was an Emeritus Conductor of the Orchestra of the Age of Enlightenment, and chief conductor of the Orchestra of the Eighteenth Century.
His recordings include, as a flautist, selections from the Pièces de Clavecin en Concerts of Jean-Philippe Rameau, and as a conductor, symphonies of Beethoven, Joseph Haydn and Franz Schubert.