Jan Caeyers studied musicology at the University of Leuven and flute at the Conservatories of Antwerp and Brussels. In addition to this, he studied conducting at the Hochschule für Musik und Darstellende Kunst in Vienna (AT).

From 1993 until 1997, Caeyers was Claudio Abbado's assistant at the Gustav Mahler Youth Orchestra (AT), where he also worked in close collaboration with Bernard Haitink and Pierre Boulez. Until 2003, he was the director of the Beethoven Academy, which he had founded in 1993. In 2010, he founded Le Concert Olympique, an international orchestra specialised in performing the works of Beethoven and his contemporaries.

As a freelance conductor Jan Caeyers has worked at the Opera in Stuttgart (DE) and with other European orchestras. He has also conducted choral ensembles such as the Arnold Schoenberg Choir (AT) and Nederlands Kamerkoor (NL).

Caeyers is professor at the University of Leuven and board member of the Stiftung Beethoven-Haus Bonn (DE). He is the author of a Beethoven biography.