The name is in honor of Captain William Logan, who came to Montana in 1872, taking part in General Baker’s campaign against the Indians in 1872 to 1876.

In 1877, Captain Logan accompanied General Gibbon on the expedition which resulted in the Battle of the Big Hole on August 9, 1877, where he met his death.

In addition, the Northern Pacific operated a secondary freight-only line between Logan and Bozeman, Montana from the 1920s through the 1950s.

This was eventually made redundant by the use of diesel locomotives such as the EMD FT on the Northern Pacific and the alternate route was subsequently removed.

Until the 1930s Logan was home to a six-stall roundhouse, as well as coal and water facilities which supported the Northern Pacific's steam locomotives.