Its predecessor, the Rock Island and La Salle Railroad Company, was incorporated in Illinois on February 27, 1847, and an amended charter was approved on February 7, 1851, as the Chicago and Rock Island Railroad. Construction began in Chicago on October 1, 1851, and the first train was operated on October 10, 1852, between Chicago and Joliet. Construction continued on through La Salle, and Rock Island was reached on February 22, 1854, becoming the first railroad to connect Chicago with the Mississippi River.

In Iowa, the C&RI's incorporators created (on February 5, 1853) the Mississippi and Missouri Railroad Company (M&M), to run from Davenport to Council Bluffs, and on November 20, 1855, the first train to operate in Iowa steamed from Davenport to Muscatine. The Mississippi River bridge between Rock Island and Davenport was completed on April 22, 1856.^[2]

 The former Rock Island Depot at Chillicothe, Illinois, now a railroad museum

In 1857, the steamboat Effie Afton ran into the Rock Island's Mississippi River Bridge. The steamboat was overcome by a fire, which also destroyed a span of the bridge. This accident caused a series of court cases. In one of the cases, Abraham Lincoln, a lawyer at the time, represented the Rock Island. Lincoln argued that not only was the steamboat at fault in striking the bridge, but that bridges across navigable rivers were to the advantage of the country.^[3][4]

 Aerotrain advertisement.

The M&M was acquired by the C&RI on July 9, 1866, to form the Chicago, Rock Island and Pacific Railroad Company. The railroad expanded through construction and acquisitions in the following decades.^[2]

On March 21, 1910, the Green Mountain train wreck resulted when a Rock Island Railroad passenger train derailed, killing 52 passengers and severely injuring scores of others.

The railroad retired its last steam locomotive from service in 1953.