After the Civil War, Scott was heavily involved in investments in the fast-growing trans-Mississippi River route into Texas, with long-term plans for a southern transcontinental railway line connecting the Southern states and California. From 1871 to 1872, Scott was briefly the president of the Union Pacific Railroad, then the first transcontinental railroad owner. He was the president of the Pennsylvania Railroad from 1874, upon the death of his partner Thomson, until 1880. The financial Panic of 1873 and subsequent economic depression made it impossible to finance Scott's southern transcontinental railroad plans.