When he was just 14 or 15 years old, Samuel went to fight in the Civil War, on the Union side. He joined the 87th Regiment of the Illinois Infantry Volunteers, in August of 1862; he was a private in Company I. The minimum age to enlist was 18, and so he must have lied on the military paperwork. His father was then 76 years old and a widow, and so Samuel probably enlisted without his father's permission. He enlisted in Shawneetown, which was 40 miles south of Carmi, where he lived with his father and sister.

The regiment mustered in, on October 3, 1862. In January of 1863, the regiment left for Memphis, Tennessee. The weather was extremely cold, and measles broke out among the troops. Two hundred and fifty men died. In Tennessee, they got on a steamboat called the Crescent City, and they went down the Mississippi River to Louisiana. They fought the Confederate Army in several battles, in Louisiana and Mississippi, including the Siege of Vicksburg.

On April 8, 1864, the regiment took part in the Battle of Sabine Cross Roads, and although they were badly defeated, it was said that they marched off the battlefield in regimental formation.

They then headed south to Alexandria, Louisiana, in the central part of the state, along the Red River, and they were involved in several smaller battles, while they occupied Alexandria. On May 2, 1864, Samuel and his regiment fought at Wilson's Landing and Chambers Plantation. These battles took place along the Red River, near where the Louisiana State University is now located.

It is believed that Samuel was badly injured that day, and that he was then sent to a military hospital in New Orleans. A few of the hotels there had been converted into hospitals during the war, including the St. James Hotel and the Saint Louis Hotel. He died in one of those hospitals, on May 4, 1864. He was only 16 or 17 years old. The records do not indicate where he was buried, but it is suspected that he was buried in the Chalmette National Cemetery, in New Orleans, in one of the 7,000 unmarked graves. That cemetery opened in May of 1864.

His half-nephew, William F. Draper, who enlisted with him and was in the same regiment, but in Company G, died on April 7, 1864, at the Battle of Wilson's Farm, and he was buried at the Alexandria National Cemetery.