Fagen was born in New York City on February 24, 1951. He began conducting studies there with Laszlo Halasz and later enrolled at Curtis Institute, where he studied under Max Rudolf. He took further courses at the Salzburg Mozarteum and studied with Hans Swarowsky in Vienna. At 23, Fagen won the first Baltimore Symphony Orchestra Conductors Competition; he also won Italy's Gino Marinuzzi International Conductor Competition. Following his Baltimore win, Fagen became an assistant at the Frankfurt Opera under Christoph von Dohnányi and at the Met under James Levine. From 1989-2004, Fagen served as the music director of the Queens Symphony Orchestra. Fagen also held conducting posts in Kassel and Brunswick, Germany, and served as the chief conductor of the Flanders Opera.
From 2002-2007, Fagen was the music director of the Dortmund Philharmonic and Dortmund Opera. In the 2008-2009 season, he was the principal guest conductor of Italy's Haydn Orchestra. Beginning in 2008, Fagen has served as a professor of music at the Indiana University Jacobs School of Music. In 2010, he was appointed the music director of the Atlanta Opera. Fagen has guest conducted major orchestras around the world, including the Tokyo Philharmonic, Czech Philharmonic, Baltimore Symphony, Munich Radio Symphony, and major orchestras in Israel, Italy, South America, and elsewhere. As a conductor of opera, Fagen has a repertory of more than 70 operas and has led performances of the major works of Verdi, Puccini, Wagner, Strauss, and Mozart, as well as lesser-known fare by Menotti (Maria Golovin), Glass (Akhnaten), and others. In the concert realm, his repertory is similarly broad, taking in many of the standards but also including less popular fare like the symphonies of Martinu and concertos of Edward MacDowell.
Fagen has primarily recorded for Naxos, though he has also recorded for RCA and Thorofon. One of his earliest recordings was a 1997 Naxos disc of The Caucasian Sketches and other works by Ippolitov-Ivanov. Fagen's more acclaimed recordings include a pair of 2010 Naxos releases containing the complete piano concertos of Bohuslav Martinu, with the Bohuslav Martinu Philharmonic Orchestra and pianist Giorgio Koukl. Fagen led the ORF Vienna Radio Symphony in a pair of Naxos recordings in 2020: one of music by Morton Gould and one of music by William Dawson and Ulysses Kay. ~ Robert Cummings & Keith Finke, Rovi