By 1874 the line had been expanded north to Middleton and four years later the name changed to Ship Island, Ripley & Kentucky Railroad.

The northern division of the Gulf and Ship Island railroad was also purchased, expanding the line to Pontotoc, Mississippi.

In 1903, the Mobile, Jackson & Kansas City Railroad started building north from Beaumont, Mississippi, and joined with the Gulf & Chicago.

In 2004 MTNR filed to abandon 43.2 miles (69.5 km) of track from a point just south of New Albany down to Houston, citing low traffic volumes and expensive maintenance costs.

In 2011, MTNR received financial support from the towns of Ripley and New Albany to make improvements to the line and began replacing rail ties.

On November 10, 2011, Alabama and Florida Railway (a subsidiary of Pioneer Railcorp) filed a petition to acquire and operate the MTNR.