Watkins was born on June 26, 1839 near Columbia, Maury County, Tennessee, and received his formal education at Jackson College in Columbia. He originally enlisted in the “Bigby Greys” of the 3rd Tennessee Infantry in Mount Pleasant, Tennessee, but transferred shortly thereafter to the First Tennessee Infantry, Company H (the “Maury Greys”) in the spring of 1861. Samuel's brother, David Watkins, served in the First Tennessee Cavalry, commanded by (among others) Colonel J. H. Lewis.