The route is a combination of the remnants three former lines: the Seaboard Air LineAtlanta-Birmingham main line, the Louisville and Nashville Railroad former Mineral Belt line from Birmingham to Gadsden and Talladega, and the Nashville, Chattanooga and St. Louis Railway line from Guntersville to Attalla, which once went further north to Huntsville using a car ferry over the Tennessee River. All of these lines eventually fell under the ownership of CSX. CSX and its corporate predecessors abandoned the L&N line south of Wellington, Alabama, where it crossed over the SAL main line; later the SAL line was abandoned from Wellington to Atlanta. The portion of the former L&N line from just north of Attalla (at its junction the NC&StL line) through Oneonta to Birmingham was sold to a quarry owner along the line, who intended to operate it as an independent shortline. Almost all of the line was later abandoned, leaving an L-shaped line from Birmingham to Guntersville. CSX operated this as the Alabama Mineral Subdivision.
In 2004, CSX leased the line to Omnitrax, which gave the line its current name. According to Omnitrax, there are more than three dozen online customers. The line includes a short branch to Ivalee, Alabama which serves a Tyson Foods feed plant; this branch is a stub of the former L&N line to Birmingham. ATN interchanges with CSX at Boyles Yard, and with Norfolk Southern (former Southern Railway) at Attalla.