The first rail station in Flagstaff was built in 1886 by the Atlantic and Pacific Railroad. That wooden depot burned down and was replaced in 1889 by a stone building that still stands. The Atchison, Topeka and Santa Fe built the present depot in 1925, and a public celebration was held on January 5, 1926.
The first trains used the new depot on January 6, 1926. Across San Francisco Street at 101 East Route 66 is the 1889 solid red sandstone depot that the 1926 one replaced. It became a freight depot afterward.
Amtrak took over passenger service on May 1, 1971 and runs the station from the 1926 depot, which also holds the Flagstaff Visitor Center. The Southwest Chief stops here daily.

