Letonja was born in Slovenia's second city of Maribor on August 12, 1961. When he was young, he was interested primarily in rock music, but a high school music teacher won him over to the classics by having him conduct his high school's orchestra. Letonja studied conducting and piano at the Academy of Music in Ljubljana; among his conducting teachers there was Anton Nanut. He went on to the University of Music and Performing Arts in Vienna, studying conducting with Otmar Suitner and graduating in 1989. It did not take long for Letonja to find a major professional position; from 1991 to 2003, he was music director of the Slovenian Philharmonic Orchestra.
In 2003, Letonja took a dual position as music director of the Sinfonieorchester Basel and music director and chief conductor of Theater Basel, leading operatic performances. He was active in both orchestral music and opera in the 2000s decade, appearing at other major opera houses, including La Scala, the Semperoper in Dresden, and the Staatsoper in Berlin. With the Sinfonieorchester Basel, he made his recording debut, issuing a cycle of the symphonies of Felix Weingartner that continued even after he left his post with the orchestra in 2006. Letonja served as the principal guest conductor of the Orchestra Victoria Melbourne from 2008 to 2011 and also conducted productions at the Stuttgart State Opera in Germany during this period. He has guest conducted other orchestras such as the Munich Philharmonic, the Vienna Symphony, and the West Australian Symphony. In 2012, Letonja became the chief conductor of the Orchestre Philharmonique de Strasbourg in France, holding that post until 2021 and making several recordings with that group, including a 2022 album featuring Janácek's Glagolitic Mass. Since 2019, Letonja has been music director of the Bremen Philharmonic. ~ James Manheim, Rovi