Born in 1957 in Haifa, she studied composition at the Samuel Rubin Israeli Academy of Music, with Dieter Schnebel in Berlin on a DAAD scholarship, and with Roger Reynolds in San Diego. She has participated in the International Summer Courses for New Music in Darmstadt, including as a lecturer (1990–2000). In 1997–2005 she was professor of composition at the University of California in San Diego, and in 2005–9 she lectured at the University of Music and Performing Arts in Vienna. Since 2003, she has run a summer academy for young female composers at Schloss Solitude near Stuttgart (where she had held a scholarship in 1996). In 2009 she became Walter Bigelow Rosen Professor of Music at Harvard University. Since 2010 she has regularly taught composition at the Tzlil Meudcan International Festival and Summer Courses for New Music in Tel Aviv. 

Her numerous accolades include the Kranichsteiner Musikpreis, Asahi Shimbun Fellowship Prize, Ernst von Siemens Music Foundation Prize, Rockefeller Foundation Prize, Fromm Foundation Award, Guggenheim Fellowship Award, Heidelberger Künstlerinnenpreis, and GEMA Award. Her chamber opera Pnima... ins Innere, staged at the 2000 Munich Biennale, won the Bavarian Theatre Award and was selected as the best world premiere of the year by Opernwelt, which reiterated the honour in 2007 for Infinite Now. In 2005 and 2006, she was composer-in-residence at the Salzburg Festival, and in 2013 at the Lucerne Festival. In 2021, her composition Unhistoric Acts was premiered for the 100th anniversary of the Donaueschingen Musiktage. 

Chaya Czernowin is a member of the Academy of the Arts in Berlin, the board of the European Music Theatre Academy, and the Bavarian Academy of Fine Arts. 

Selected works (from 2013): At the fringe of our gaze for orchestra and concertino group (2012–13), White Wind Waiting for guitar and orchestra (2013), HIDDEN for string quartet and electronics (2013–14), Knights of the Strange for ensemble (2014; version for electric guitar and accordion, 2015), Winter Songs Version IV: Wounds/Mistletoe for two septets and three percussionists (2014), Winter Songs Version V: Forgotten Light for two septets and octet with two singers (2014), Infinite Now, opera (2015–16), On the Face of the Deep for large ensemble (2017), Guardian for cello and orchestra (2017), Habekhi (The Crying) for low female voice, ensemble and electronics (2018), Heart Chamber, opera (2017–19), Irrational for baritone, bass clarinet, trumpet and trombone (2018–19), The Fabrication of Light for large ensemble (2020), Fast Darkness I: I can see your turned eyes from inside your body for bass clarinet and ensemble (2020), Fast Darkness II: I freeze and melt for bass clarinet and large ensemble (2020), Atara, lament for orchestra and two amplified voices (2020–21), Unhistoric Acts for mixed choir and string quartet (2021), Immaterial for six voices (2021), Seltene Erde: alchimia communicationis for large ensemble and double bass with own recording (2022).