Jacqueline Fontyn was born in Antwerp, where, at the age of five, her parents entrusted her to the wonderful Russian piano teacher Ignace Bolotine. She had lessons daily, and Bolotine encouraged her to develop her taste for improvisation. At the age of fifteen, she decided to become a composer. She received her grounding in the techniques of composition from Marcel Quinet in Brussels. She continued her musical education in Paris with Max Deutsch, a fervent disciple of Schoenberg.

In 1956 she attended Hans Swarowsky's conducting class at the Akademie für Musik und Darsteliende Kunst in Vienna.

From 1963 to 1970 she was Professor of Music Theory at the Royal Conservatory of Antwerp. From 1970 to 1990 she taught Composition at the Royal Conservatory of Brussels.

She is a regular guest of universities and conservatoires in Europe (Germany, France, Hungary, The Netherlands, Poland and Switzerland), the United States, Israël, Egypt, Asia (China, Korea, Singapore, Taiwan) and New Zealand.

She has received many awards, most notably the Spanish Oscar Espla Prize and the Prix Arthur Honegger from the "Fondation de France". She was asked to write the set piece, a Violin Concerto, for the finals of the 1976 Reine Elisabeth International Music Competition, and has twice undertaken commissions from the Koussevitsky Music Foundation in the Library of Congress, Washington.

Since 2006 most of her manuscripts are hosted in the music division of the library of Congress in Washington. in 2014, the Royal Library of Belgium acquired most of the manuscripts left in the country.

Jacqueline Fontyn is a member of the Belgian Royal Academy and in 1993 the King of Belgium granted her the title of baroness in recognition of her artistic merit.