The railroad was the product of nearly 150 predecessor lines that were combined, reorganized and recombined beginning in the 1830s, formally becoming the Southern Railway in 1894.

The pioneering South Carolina Canal and Rail Road Company, Southern's earliest predecessor line and one of the first railroads in the United States, was chartered on December 19, 1827, and ran the nation's first regularly scheduled steam-powered passenger train – the wood-burning Best Friend of Charleston – over a six-mile section out of Charleston, South Carolina, on December 25, 1830.

[2][3] The company leased enslaved African Americans from plantation owners when free white people refused to work in the swamps.

[4] As railroad fever struck other Southern states, networks gradually spread across the South and even across the Appalachian Mountains.

[5] The Western North Carolina Railroad was halted because voters were angry about that law allowed purchasers of private bonds to have the train tracks veer to their towns.

Five-hundred African Americans were assigned to provide backbreaking labor on the Western North Carolina Railroad.

[10] During his 12-year term, the railway built new shops at Spencer, North Carolina, Knoxville, Tennessee, and Atlanta, Georgia, upgraded tracks, and purchased more equipment.

[10] He moved the company's service away from an agricultural dependence on tobacco and cotton and centered its efforts on diversifying traffic and industrial development.

[11] After the line from Meridian, Mississippi, to New Orleans, Louisiana, was acquired in 1916 under Southern's president Fairfax Harrison, the railroad had assembled the 8,000-mile, 13-state system that lasted for almost half a century.

[10] Despite these small acquisitions, the Southern disdained the merger trend when it swept the railroad industry in the 1960s, choosing to remain a regional carrier.

Starting in 1833, its predecessor, the South Carolina Canal and Rail Road, was the first to carry passengers, U.S. troops and mail on steam-powered trains[22] and experimented with railroad lighting.

They had a pine log fire on a flatcar, covered in sand, to provide light at night before inexpensive kerosene was invented for lamps.

Another new shop site was established on the north side of Birmingham, Alabama near the Findley Yard in 1924, taking the place of two obsolete facilities.

[24] The Southern Railway began dieselization in 1941, and was the largest all-diesel railroad when it retired its last steam locomotive in 1953.

In the early 2000s, a 22-mile (35 km) loop of former Southern Railway right-of-way encircling central Atlanta neighborhoods was acquired and is now the BeltLine trail.

When Amtrak took over most intercity rail service in 1971, Southern initially opted out of turning over its passenger routes to the new organization.

Under a longstanding haulage agreement inherited from Penn Central and the Pennsylvania Railroad, Amtrak carried the train north of Washington.