In 1859 he taught in a 'Deaf and Dumb Asylum' in Baton Rouge, Louisiana, while in 1869 he spent time travelling around Europe.

[1] He then enrolled to study theology at Berkeley Divinity School and graduated in 1861.

Thomas was ordained deacon on May 17, 1861, by Bishop Thomas M. Clark at St Paul's Church in Wickford, Rhode Island, and then priest on April 5, 1862, at St Paul's Church in New Haven, Connecticut, by Bishop John Williams.

Between 1861 and 1864, he served as rector of St Paul's Church in New Haven, Connecticut, and then in 1864, he was elected rector of Seabury Divinity School in Faribault, Minnesota, and in 1865 he became Professor of Biblical Exegesis and Hebrew.

[3] Thomas was elected Assistant Bishop of Kansas on the first ballot on February 2, 1887.