His father, Joseph Smith III, died on December 10, 1914, leaving the Reorganized Church without a leader. However, the leadership of Frederick Madison Smith was accepted shortly afterwards, and so he became the second President of the Reorganized Church in 1915. Smith was known for his interests in applying the principles of the newly emerging fields of sociology and social welfare to the Church's thinking on the principles and doctrine of Zion. He became embroiled in a controversy over Supreme Directional Control of the Church that led to a major loss in membership. He also presided during the difficult depression years which stalled construction of the Auditorium as the church faced issues of major financial debt.
Frederick M. Smith became the first president of the church to submit notice of resignation. However, he never ceased to be president of the church on account of the fact that the General Conference who he submitted his resignation to, rejected it (see page 227 of The Church Through the Years, Vol. II, by Richard P. Howard, Herald Publishing House, Independence, MO., 1993).
The Frederick Madison Smith Library is one of two libraries belonging to Graceland University, and is located on their Lamoni campus. It opened in 1966.