He entered the general theological seminary of the Protestant Episcopal Church, where he completed his work and was ordained deacon on June 29, 1862.

On September 1, 1868, he was called to the rectorship of St. James Parish in Batavia, New York, and two days later was elected Bishop of the Diocese of Missouri.

Robertson rapidly became an influential member of the House of Bishops, and was honored with a full share of the labors connected with the administration of the general institutions of the church.

He was responsible for the establishment of the Parochial Trust Fund (now the Corporation of the Episcopal Diocese of Missouri) to hold the title to church property.

Charles Franklin Robertson established a school for girls that lasted more than 40 years and provided young women with a classical education, and also founded the first Diocesan newspaper in 1870, which was published until the 1930s.