Although his early career as a music critic was clouded by the negative influence of his teacher, Zdeněk Nejedlý, with whom he studied at Charles University.
After accepting a post in 1922 as professor of musicology at Masaryk University in Brno, he went against Nejedlý's teachings and championed the music of Leoš Janáček.
Studie o české hudební tvořivosti (Czech Modern Music: A study of Czech musical creativity, 1936), came under public attack by Nejedlý and his remaining followers.
During the Nazi occupation, Helfert became involved with the underground Czechoslovak Communist Party and was arrested for resistance activities.
He was interned in Brno's Špilberk Castle by the Gestapo in 1939, and subsequently in Wrocław until 1942.