The railroad’s official paint scheme contains yellow and navy blue colors arranged in much the same way as the colors on the "yellowbonnets" that once operated on the Atchison, Topeka and Santa Fe Railway were arranged. The words "Northern Plains" are spelled out on both the nose and the long hood. Many of the locomotives operating on the Northern Plains Railroad continue to wear the colors of their former owners. This includes at least four former Union Pacific Railroad EMD SD40T-2 locomotives.