In 1960, his father took him to a performance of Beethoven's Pastoral Symphony conducted by Tibor Paul,[1] from which he decided to become a conductor.

[3] Challender succeeded Zdeněk Mácal as chief conductor of the Sydney Symphony Orchestra from 1987 to 1991, to great acclaim.

In Australia's bicentennial year (1988), he led the orchestra in a successful tour of the United States, a 12-city tour that culminated with a concert at the United Nations General Assembly in New York to mark 200 years of European settlement in Australia.

[4] In June of that year, his health visibly failing, Challender conducted his last concert in Hobart, with the Tasmanian Symphony Orchestra.

[3] One week later, on 20 December, at the Sydney Town Hall, Justice Michael Kirby led the speakers at a celebration of Challender's life.

A seven-minute piece for solo cello by Peter Sculthorpe titled Threnody: In memoriam Stuart Challender was performed by David Pereira.