At the outbreak of the American Civil War, Hodgson left seminary and enlisted as a private in the 44th Virginia Infantry of the Confederate States Army. He transferred to serve in the 1st Regiment Alabama Infantry, which was led by his brother, Colonel Joseph Hodgson. He was eventually promoted to the staff of General Joseph Wheeler. In 1863 he was ordained as an Episcopal deacon and then as a priest in 1864 in Macon, Georgia, where he served as a chaplain in a hospital. A few years after the war, Hodgson went to Europe, where he lived in 1869–1870.
