Born in Los Angeles in 1969, Stockhammer studied composition with Ian Krouse and Stephen Hartke and conducting with Daniel Lewis. While still a student, he had the opportunity to step in for a series of concerts with the Los Angeles Philharmonic and was subsequently mentored by principal conductor Esa-Pekka Salonen. He later moved to Germany, where he still lives today.

Current highlights in Jonathan Stockhammer's schedule include Mahler's Symphony No. 2 with the Seoul Philharmonic at the opening of the 2025 PyeongChang Festival, his debut with the London Symphony Orchestra with works by Debussy, Ravel and Adams, and the new production of Philip Glass' Akhnaten (director: Barrie Kosky) at the Komische Oper Berlin. For his debut with the Yomiuri Nippon Symphony Orchestra, he conducted Mahler, Mendelssohn and Haas at Tokyo's Opera City. He has also conducted Mahler's Symphony No. 6 at the Vienna Musikverein, Mahler's Das Lied von der Erde at the Ljubljana Festival, Lutosławski's Concerto for Orchestra with the Bremen Philharmonic, Tchaikovsky's Eugene Onegin with the Staatskapelle Berlin, and a mini-festival of violin concertos by Berg, Stravinsky, Bartók, Prokofiev, Schoenberg and Hartmann with Patricia Kopatchinskaja and the Dresden Philharmonic. His musical direction of Kirill Serebrennikov's new production of Alfred Schnittke's Das Leben mit dem Idioten (Life with the Idiot) at the Zurich Opera House earned him effusive praise: ‘Conductor Jonathan Stockhammer guides us through the depths of the piece like someone who can easily convince us of any musical style’ (SRF2 Kultur).

In the 2025/26 season, Stockhammer will make his debut at the Bayreuth Festival, where he will take over the musical direction of Bernhard Lang's world premiere Brünnhilde brennt in cooperation with the Dortmund Opera. He will also conduct Tchaikovsky's Symphony No. 3 with the German Radio Philharmonic Saarbrücken Kaiserslautern, tour with the German National Youth Orchestra and the German National Youth Jazz Orchestra, and conduct Sibelius' Symphony No. 2 with the Bremen Philharmonic Orchestra. He will also return to the Staatskapelle Dresden and the Norwegian Radio Orchestra and will work with the Hamburg Symphony Orchestra, the Bilkent Symphony Orchestra, the Ensemble Modern and the Dresden Sinfoniker.