He obtained a charter for a new railroad to run from Atchison, Kansas to the state capital at Topeka in 1859. In 1863, Holliday decided to extend the railroad along the route of the Santa Fe Trail to Santa Fe, New Mexico. Once there he intended it to go all the way to the Pacific Ocean in California. The name of the railroad was changed to the Atchison, Topeka and Santa Fe Railroad Company (AT&SF). A severe drought followed by the Civil War starting in 1861 prevented the railroad from making much progress. The line was completed through Kansas by December 1872. By 1880, the line was completed to Santa Fe. The railroad experienced hardships in 1893 and almost had to declare bankruptcy. Holliday was able to refinance and reorganize the railroad. He remained president of AT&SF until his death on March 31, 1900.