He did not initially intend a career in the clergy, but he afterward went to North Carolina and studied for the ministry of the Episcopal Church.

Freeman was ordained deacon in Christ Church, Raleigh, North Carolina, by Bishop John Stark Ravenscroft in 1826, and was ordained priest in New Bern, North Carolina the following year by the same bishop.

In 1829, Freeman was elected rector of Christ Church, Raleigh, and served in that office until 1840.

After a short stay in Swedesboro, he accepted a call to become rector of Immanuel Church, New Castle, Delaware.

He was soon afterward elected missionary bishop of Arkansas and the Indian Territory, and was consecrated in St. Peter's Church, Philadelphia, October 26, 1844.