Märkl studied piano and the violin as a youth. Beginning in 1978 at the Musikhochschule Hannover he continued his piano and violin studies and also began to study conducting. He later attended the University of Michigan where his mentors included Gustav Meier. He was also a pupil of Sergiu Celibidache. He later won a conducting stipend to Tanglewood, where he was under the tutelage of Leonard Bernstein and Seiji Ozawa.
From 1991 to 1994 Märkl served as Music Director of the Saarländischen Staatstheaters (Saarland State Theatre) in Saarbrücken. From 1994 to 2000, he was Generalmusikdirector and director of opera at the Mannheim National Theatre. In the U.S. he made his Metropolitan Opera conducting debut in February 1999 with Il trovatore, and returned in December 2000 with Turandot.
In 2005, Märkl became music director of the Orchestre National de Lyon (ONL). With the ONL, he has conducted several recordings for the Naxos label, including music of Claude Debussy, Maurice Ravel, and Olivier Messiaen. Märkl concluded his ONL tenure in 2011. In September 2007, he became principal conductor of the MDR Symphony Orchestra in Leipzig. Märkl resigned from this post after the 2011-2012 season. He became musical advisor to the Basque National Orchestra (Orquesta de Euskadi) effective with the 2014-2015 season. In November 2014, the orchestra elevated Märkl's title to chief conductor with immediate effect, through the 2015-2016 season. He is scheduled to conclude his tenure with the Basque National Orchestra in June 2017.
- John Rockwell (4 August 1987). "Perle's 'Songs' At Tanglewood Festival". New York Times. Retrieved 2007-09-08.
- Anthony Tommasini (15 February 1999). "The Met Takes Up A Verdian Challenge". New York Times. Retrieved 2007-09-08.
- Anthony Tommasini (14 December 2000). "A Soprano Put to the Test Shifts in Tone and Intensity". New York Times. Retrieved 2007-09-08.
- Andrew Clements (2008-05-30). "Debussy: La Mer; Prélude à l'Après-Midi d'un Faune; Jeux; etc, Orchestre National de Lyon/ Märkl". The Guardian. Retrieved 2009-12-25.
- Tim Ashley (2010-09-09). "Debussy: Le Martyre de Saint Sébastien / Khamma". The Guardian. Retrieved 2011-08-10.
- Stephen Pritchard (2011-06-19). "Debussy: Orchestral works Vol 6 – review". The Observer. Retrieved 2011-08-10.
- Tim Ashley (2009-08-14). "Ravel: Daphnis et Chloé; Shéhérazade Overture". The Guardian. Retrieved 2009-12-25.
- "MDR stellt neuen Chefdirigenten vor" (Press release). MDR. 18 April 2011. Archived from the original on 2 April 2012. Retrieved 2011-11-06.
- "La Orquesta Sinfónica de Euskadi buscará su 'personalidad sonora' de la mano del director Jun Markl". El Mundo. 2014-06-16. Retrieved 2014-09-20.
- "Jun Märkl named chief conductor of the Basque National Orchestra" (Press release). Basque National Orchestra (Euskadiko Orkestra). 3 November 2014. Retrieved 2015-09-26.
- "Robert Treviño, appointed music director of the Basque National Orchestra" (Press release). Basque National Orchestra. 2016-11-03. Retrieved 2017-01-05.
- Official webpage of Jun Märkl
- MusicVine agency biography of Jun Märkl
- Robert Hugill, Review of Naxos 8.572174. Music Web International website, 10 March 2010
|Music Director, Orchestre National de Lyon
|Chief Conductor, MDR Sinfonieorchester
|Principal Conductor, Euskadiko Orkestra