From 1875 to 1877 he attended the Leipzig Conservatory where he studied music under Carl Reinecke, Salomon Jadassohn, and Ernst Friedrich Richter.
In 1878 Zöllner became the director of music at the University of Dorpat (now Tartu) in Estonia where he stayed for almost seven years. In 1885 he joined the faculty at the Cologne Conservatory and while there he conducted the Cologne Male Voice Choir. Zöllner moved to the United States in 1890 to become the conductor and director of the Deutscher Liederkranz in New New York
Zöllner returned to Leipzig in 1898 to replace Hermann Kretzschmar as director of music at Leipzig University, taking over the Paulus male choir.
Four year later he was appointed professor of composition at the university as a replacement for his mentor, East.F. Reinecke. From 1903 to 1906 he was the editor of the Leipzig Tageblatt.
He was conductor of the Flemish Opera in Antwerp from 1907 until his retirement in 1914. He retired to Freiburg and worked part-time as an opera critic for the Breisgauer Zeitung.