[3] After the outbreak of the Civil War, Georgia Governor Joseph E. Brown appointed Harrison a brigadier general of state troops to rank from September 14, 1861.

[3] Harrison did this, and led a force guarding the Georgia coast, during the winter of 1861–1862, after which his command was terminated.

[3] Under a new militia law in 1864, Harrison was appointed colonel in charge of Georgia's First Military District with the duties of destroying whiskey stills and tracking down deserters.

[3] When they reached the Savannah area, Sherman's men pillaged Harrison's home and property at Montieth.

[2][3] Harrison was released from prison before the end of the war but refused to take the oath of allegiance to the United States government.