Nathaniel Thomas was born into slavery around 1820 in Albemarle County, Virginia. He spent most of his early life in Missouri, where he was owned by a farmer named William Darrett. He married Winnie Fields in Marshall, Missouri, around 1842, and they had at least two children together: Ann, born February 1853; and Jerry, born around 1855. Thomas enlisted in the Union army in Marshall on March 19, 1864, and mustered in as a private in Company G of the 68th USCT Infantry Regiment later that month. His enlistment records describe him as 5 feet, 2 1/2 inches tall, with black hair, black eyes, and a black complexion. Thomas contracted smallpox and rheumatism in Memphis, Tennessee, in April 1864 and spent the next 4 months recovering in a St. Louis hospital. Thomas eventually rejoined his regiment, but he suffered from recurring bouts of rheumatism. He experienced such difficulty marching that the army detached him to assist the cook. He received a discharge for disability on June 24, 1865, in Greenville, Louisiana.

After his discharge, Thomas spent the rest of his life in Saline County, Missouri. He performed farm work until 1872, when back pain left him debilitated. He then remained primarily confined to his house, and his eyesight failed in September 1887. Thomas began receiving a $4 monthly pension in May 1889, and the government eventually increased the amount to $12 per month. Winnie Thomas died on January 12, 1889, and Nathaniel Thomas followed a year later, around February 1900.