When railroads came to the area he first went to work as Chief Engineer of the California Southern Railroad, a company chartered to build a rail line between San Diego on the coast and Barstow in the desert. When it was taken over in a merger, he advanced to Chief Engineer of the Atchison, Topeka and Santa Fe Railway. In 1885 he oversaw the construction of the railroad through the difficult Cajon Pass, between the San Gabriel Mountains and San Bernardino Mountains east to the Mojave Desert. It is a route that is still in use by BNSF Railway and Union Pacific Railroad, and the pass by the Interstate 15 highway. Perris held the Chief Engineer position with Santa Fe for 35 years.