As a youth, Fickénscher studied music overseas in Munich with Ludwig Thuille and Josef Rheinberger. Having completed his course of study in 1896, Fickénscher took up residence in San Francisco and worked primarily as a piano accompanist -- regarded one of the best in the business; Fickénscher toured in this capacity with such singers as David Bispham, Ernestine Schumann-Heink, and Amalie Materna. Fickénscher married the singer Edith Cruzan in 1901. In addition to his work as an accompanist, Fickénscher worked as a vocal coach and conductor, and appeared in solo recitals throughout the United States. In 1911 Fickénscher established a studio for vocal study in Berlin; however, the outbreak of war forced his return to the United States three years later. In 1920, Fickénscher was named music department head at the University of Virginia, a post he held until his retirement in 1941. At Virginia he participated as conductor and organizer of the McIntire concerts series, which brought him into contact with many of the musical lights of the day, including cellist Pablo Casals, violinist Jascha Heifetz, singer Rosa Ponselle, and others.
Fickénscher began to work with microtonal tunings in the 1890s; practically all of Fickénscher's pre-1906 musical works were destroyed in the San Francisco earthquake and fire that year. Fickénscher later summarized the results of his early experiments in two string quintets, the Evolutionary Quintet and From the Seventh Realm (1939). Composer Percy Grainger acclaimed the latter work as "unique in its sustained, rapturous mood, and the most spiritual music written at any period for this combination." In Germany in 1912, Fickénscher patented the first version of his microtonal keyboard, the polytone. Fickénscher applied in 1941 for a new polytone patent; this three-manual instrument could play 60 tones to the octave, and was capable of producing "pure" intervals of fourths and fifths in just-intonation. The improved polytone Fickénscher built in 1941 still exists at the University of Virginia, along with his papers and artifacts.
Fickénscher's surviving output includes several orchestral works, ranging from song cycles to symphonic poems such as The Day of Judgment (1927) and Variations on a Theme in a Medieval Style (1931). Fickénscher also composed sacred music, chamber works, songs and several pieces specifically composed for the polytone. Shortly before his death at age 83, Fickénscher made limited edition recordings of From the Seventh Realm and his song cycle Willowwood (1910) for the short-lived San Francisco-based Music Library Recordings imprint.