In October 1861, Foraker left his parents' home to go to the county seat of Hillsboro where he was to live with his uncle, James Reece, auditor of Highland County, and work as a clerk in his office. He was sent to replace his older brother, Burch, by then enlisted in the Union Army as the American Civil War was raging. Foraker noted in his memoirs that while his time as auditor's clerk greatly improved his penmanship, it also brought him into contact with many county officials, teaching him how a government worked. The young clerk was impressed by his brother's letters home, and was anxious to join the army despite his youth. Soon after his 16th birthday, Joseph Foraker learned that a family friend was organizing a volunteer company, and sought to enlist. His uncle gave reluctant consent, and on July 14, 1862, Foraker was mustered in Company "A", 89th Ohio Volunteer Infantry; in late August, after training, he became second sergeant. With Confederate forces moving through Kentucky and threatening Cincinnati, the 89th was hurried into defenses set up across the Ohio River in Newport, Kentucky. The Confederates did not reach the Ohio, having been forced back well to the south, and the 89th moved to Fort Shaler, near Newport. While Foraker was at Fort Shaler, President Lincoln issued the Emancipation Proclamation; Foraker recounted in his memoirs that he and his comrades felt that the proclamation meant that they were fighting for the end of slavery, not just to preserve the Union.