The NCRy features public excursions with both steam and diesel locomotives along a well-preserved portion of the first transcontinental railroad.

By 1866, the Western Pacific had built 20 miles (32 km) of track north and east from San Jose, reaching halfway into what was then known as Alameda Cañon, to about Farwell near milepost 33.

[2] The Western Pacific used 500 Chinese laborers to grade and construct the rail line into the rugged canyon with its tight curves and narrow banks.

In June 1869, J. H. Strobridge and crew began to lay out a new line starting at a point on the 1866 Western Pacific rails in the west end of Alameda Cañon (San Jose Junction at MP 30.6) westward out of the canyon towards Oakland, while Turton, Knox & Ryan dispatched workers to continue the railroad in Alameda Cañon eastward from the point where the 1866 Western Pacific rails abruptly stopped.

On November 8, 1869, the intended western terminus opened at the Oakland Long Wharf, from which ferries connected to San Francisco.

[9] Meanwhile, in 1869 Central Pacific renamed the station for their railroad attorney and stockholder, Addison Niles, who later became associate justice on the California Supreme Court.

[10] When built, the rail line through Niles Canyon was the primary route for overland traffic to and from the San Francisco Bay.

A shorter rail line between Oakland and Sacramento was established via the California Pacific Railroad and a train ferry at Benicia by 1879.

[2]: 87 The decline in San Francisco's status as a port with the advent of containerization,[11] combined with the movement of produce traffic to the highways once again left the railroad through Niles Canyon with little business.

The organization continues its work to extend and maintain the track along the line; restore its collection of railroad equipment; and operate historic demonstration trains for the benefit of the public.

The railway was determined to be eligible under National Register Criterion C to reflect the engineering significance of the resources as fine examples of historic period railroad design,[1] and under Criterion A to reflect its association with the construction of the Original Transcontinental Railroad and its role as an important freight railway in the early part of the 20th century.

Non-contributing resources consist of things built or altered since 1958, and include non-historic track, buildings, a gas pipeline, and a fiber optic line.

Previously, the Golden Gate Railroad Museum moved its collection from San Francisco to the NCRy in 2007 for storage and limited operations after their home at Hunters Point Naval Shipyard was shut down for redevelopment.

[14] In July 2021, plans were announced to move Southern Pacific steam locomotive 2479, a water tower, a round house and turntable from the California Trolley and Railroad Corporation to the NCRy.