The California Southern Railroad, a subsidiary of the Atchison, Topeka and Santa Fe Railway, chose National City as the West Coast base of operations at the terminus of their planned transcontinental railroad.

On November 14, 1885, the first transcontinental passenger train departed National City en route to the east coast.

[2] In 1889, Santa Fe moved their workshops and offices to San Bernardino and Los Angeles and operations significantly declined at National City.

The building was restored to its original condition in 1997 by the San Diego Electric Railway Association,[3] who opened it as a museum.

It is also listed as a California Historical Landmark under the name National City Santa Fe Rail Depot.