Charles Woodruff Shields and Narcissa Chisholm Owen were graduates of the Institute, and the missionary William Alexander Parsons Martin served as professor of classics for one year at the school.

In less than a year, however, Anderson was called to be Superintendent of Transportation on the Louisville and Nashville Railroad, a position in which the opening of the American Civil War found him.

In November 1861, General William Tecumseh Sherman appointed John Anderson as Railroad Director for the Department of the Ohio.

Subsequently, in November 1862, General William Rosecrans appointed Anderson military superintendent of railroads for the Department of the Cumberland.

In 1864, Anderson left the Army and became interested in the Union Pacific Railway, Eastern Division, then being planned on a route through Kansas.

He apparently never assumed control of the railroad's construction, as urged by the company's president John Perry, but he did become financially involved.

After his death, in 1908 his large Manhattan home was purchased to serve as the first Catholic school in the town, later called the Sacred Heart Academy.