Born in Strasbourg, he carried out all his studies at the conservatory of his birthplace, studying conducting with Fritz Müllch, then in Paris where he worked with Léon Barzin. For composition and orchestration, he was the student of Daniel-Lesur and Pierre Wissmer to whom he would later dedicate his Eighth Symphony.
Jean-Jacques Werner's career began in 1960 at the French Radio where, for many long years, he conducted the regional radio orchestras (Strasbourg, Nice, Lille, Toulouse, Marseilles) as well as the major Paris orchestras. From his beginnings, Jean-Jacques Werner was very anxious to make known the works of his time. In 1970, he founded the Ensemble Instrumental du Val de Marne, a group of renowned soloists for which éminent composers wrote works. In 1976, he was the first director of the EMU (Europaïsche Musikschul Union) Orchestra and would be its permanent conductor until I989. With this European ensemble, he gave numerous concerts, in particular in Switzerland, Finland, Germany, the Netherlands and France. He taught conducting from 1978 to 1982 at the Reims Conservatory and would be a guest professor at the Paris Conservatoire.
In 1981, he founded the professionally trained Jeune Philharmonie du Val de Marne with which he conducted many concerts in the greater Paris region and the provinces, also being invited to appear in Sweden, Finland, Switzerland and Germany. This ensemble would take the name of Orchestre Léon-Barzin (OLB) in 1994.
Permanent conductor and vigilant artistic director, he has appeared in concert with this orchestra of variable forces all over Europe, and radio broadcasts, festivals, and CDs attest to this intense activity.
Beginning in 1982, Jean-Jacques Werner received countless invitations to conduct and teach abroad, in particular in Taiwan, where he has gone numerous times, as well as in the USA. In 1987, he received the Prize of the Goethe Foundation in Basle with the Orchestre des 3 Frontières (Switzerland, Germany, France), in Venezuela where he went in 1982 and '83 to conduct the Falcon State Symphony Orchestra. In 1996, he conducted in South Korea, and later at the Rumanian Radio in Bucharest and Hungary.
In 2008, he was awarded one of the SACEM Prix de Printemps, the Pierre and Germaine Labolfe Prize. The following year, he was named Officier des Arts et Lettres.