The origins of the Chicago, Burlington & Quincy Railroad Company began with the Aurora Branch Railroad Company, incorporated in February 12, 1849. Stephen F. Gale of Chicago served as the company's first president, and he along with three Aurora businessmen comprised the board of directors. Service between Chicago and Aurora was inaugurated October 21, 1850, running north from Aurora twelve miles to Turner Junction (now West Chicago) to connect with the Galena and Chicago Union Rail Road, which continued to Chicago. The original Aurora Branch track was built of strap rails: thin strips of iron fixed on to wooden rails. A wood-burning "iron horse" engine, plus a one-passenger coach and two borrowed freight cars comprised the original train.

In 1952 the company changed its name to the Chicago and Aurora Railroad Company, extending the line west to Mendota, Illinois, to connect with the Central Military Tract Railroad. During this time, a group of east coast businessmen, recognizing the potential in railroads, invested in the Chicago and Aurora Branch with the intent of building the line even further west. James F. Joy, John Murray Forbes, and John Woods Brooks were among the first board of directors of the newly formed Chicago, Burlington, and Quincy Railroad Company, incorporated February 14, 1855, with lines extending nearly to the Mississippi River through lease agreements with other roads. A year later the road consolidated with the Central Military Tract Railroad and made a slight name change to the Chicago, Burlington and Quincy Rail Road Company. Over the next ten years, the company acquired existing lines and constructed new track, extending its reach over 300 miles. John Van Nortwick, formerly chief engineer of the Galena and Chicago Union Railroad, served as president from 1857-1865.