In 1980 he was engaged as a choral director at the Vienna State Opera. Soon after that he became an assistant to the music director, Lorin Maazel. During his years in Vienna he conducted the State Opera in the operas Un re in ascolto (Berio), Die Entführung aus dem Serail (Mozart), and Werther (Massenet), as well as the ballets Raymonda (Glazunov) and Orpheus (Henze).
In 1988 Schirmer was hired as principal music director of the Landeshaupstadt Wiesbaden and artistic director of the symphony concerts given by the orchestra of the Hessian State Theater. This position lasted into 1991, at which time he began to conduct more performances at the Vienna State Opera. From 1993 to 1995 he held the position of music consultant to the directors of the Vienna State Opera.
In 1995 Schirmer was appointed music director of the German National Radio Symphony, the world's oldest radio orchestra. He served in that capacity into 1998. During that time he took the orchestra on important tours through Europe and to the United States. He made his British debut leading the orchestra as guest ensemble at a BBC Proms concert in August, 1995.
After the end of his tenure with the German National Radio Symphony he embarked on some seasons as a guest conductor, including performances of Wagner's Siegfried and Götterdämmerung in Graz, and Strauss's Rosenkavalier and Berg's Lulu at Paris's Opéra de la Bastille. In 2006 he was appointed chief conductor of the Munich Radio Orchestra, and he has been music director fo the Leipzig Opera since 2009. Notable operatic recordings include Richard Strauss's Capriccio with Dame Kiri Te Kanawa, Carl Nielsen's Maskarade, Berg's Lulu, and operettas by Léhar and Nicolai.