Van Leer received his first flute at the age of eleven from his father, a classical flautist. He studied History of Art at Amsterdam University; after when he began studying flute and composition at Amsterdam Conservatorium. He received a degree for flute from Geneva Conservatoire and also studied piano, orchestration (with Rogier van Otterloo), and organ (with Anthon van der Horst).
While still at school, van Leer led a jazz group on piano. He went on to play the flute and sing with the Shaffy cabaret group. In 1969 he joined Martijn Dresden (bass) and Hans Cleuver (drums) to form a trio that covered songs by Traffic and backed other Dutch musicians, as well as playing their own material. Later in the year guitarist Jan Akkerman joined, completing the lineup of Focus. They released several albums in the early 1970s.
Van Leer headed Focus through several lineup changes, and by 1977 he was the only remaining original member. The group disbanded in 1978. In 1985, van Leer briefly reunited with Jan Akkerman to make Focus 1985. In 2002, van Leer created a new Focus line-up, which has since released the albums Focus 8 & Focus 9 / New Skin. Their British tour in spring 2006 indicates that the mastery Van Leer shows with the Hammond organ is undiminished although his vocal range is more limited than in the band's early period. The lead guitar and drumming skills evident in their set demonstrate that, despite personnel changes, Focus remain in the top league of creative rock outfits. They undoubtedly helped to break down the barriers between rock, jazz and classical styles and remain hard-to-categorize for that very reason.
In addition to his work with Focus, van Leer has released a large number of solo albums since 1972. He also appeared as a guest musician on the album Into the Electric Castle by Arjen Anthony Lucassen's musical project Ayreon.