Elert was born on August 19, 1885 in the village of Heldrungen in what is modern-day Thuringia, but he grew up in northern Germany. His parents were August Elert and Friederike, née Graf, Elert. After attending the Realgymnasium in Harburg and the Gymnasium in Husum, he studied theology, philosophy, history, German literature, psychology and law in Breslau, Erlangen, and Leipzig. He earned doctorates in philosophy and theology at Erlangen.

After working as a tutor for a short time in Livonia, he served as a pastor from 1912 to 1919 in Seefeld, Pomerania. During World War I he served as a field preacher on several fronts.

In 1919 Elert became Director of the Old Lutheran Theological Seminary in Breslau. In 1923 he was appointed to the Chair of Church History at the Friedrich-Alexander University Erlangen, now University of Erlangen-Nuremberg. With the death of Philip Bachman in 1932 he was appointed to the chair of Systematic Theology. In the academic year 1926/27 he was rector of the University and in 1928-29 and 1935-43 Dean of the Theological Faculty.

Elert retired in 1953, and he died on November 19, 1954 in his 70th year due to complications following an operation.

His former home in Erlangen, Hindenburgdamm 44, is now a theological study house "The Werner Elert Home," owned by the Evangelical Lutheran Church in Bavaria.