Chaya Czernowin was born and brought up in Israel. After her studies in Israel, at the age of twenty-five, she continued studying in Germany (DAAD grant) and the United States. She was then invited to live in Tokyo (Asahi Shimbun Fellowship and American NEA grant), in Germany (a fellowship at the Akademie Schloss Solitude), and Vienna. Her music has been performed throughout the world by some of the best orchestras and performers of new music. Czernowin has held a professorship at the University of California, San Diego, and was the first woman to be appointed as a composition professor at the University of Music and Performing Arts in Vienna, Austria (2006–9) and at Harvard University (2009 and on), where she has been the Walter Bigelow Rosen Professor of Music.

Together with Jean-Baptiste Jolly, the director of Akademie Schloss Solitude near Stuttgart, and with the composer Steven Kazuo Takasugi, Czernowin has founded the summer Academy at Schloss Solitude, a biannual course for composers. Takasugi and Czernowin also teach at Tzlil Meudcan, an international course based in Israel founded by Yaron Deutsch of Ensemble Nikel.