Like many railroad towns in the South, Madison Station was heavily damaged by the Union Army during the Civil War. Ten miles from the state capital of Jackson, Madison Station was largely destroyed in 1863 after the July 18–22 siege of Jackson. No battles were fought in Madison County, but Major General Stephen D. Lee concentrated his command in Madison Station during the month of February 1864. Stephen Lee was later appointed as the first president of Mississippi State College (now Mississippi State University).