[1][2] In conjunction with the Monticello Steamship Company, the railway offered a combined rail- and ferry-service called the "Napa Valley Route."

From there, it headed northwards for a total of 41.7 miles (67.1 km)[3]: 201  to terminate at Calistoga, passing through Napa, Yountville, Oakville, Rutherford, and St. Helena.

Construction of the railroad commenced in 1903 and trains began running from Vallejo to Napa following a grand opening on July 4, 1905.

[3]: 116 On June 19, 1913, two trains of the San Francisco, Napa and Calistoga Railway collided head-on in the worst interurban accident in the state of California.

On February 13, 1938, a farewell excursion train was operated between Vallejo and Napa for the Electric Railway Historical Society of California.

A stretch of track north of St. Helena between Greystone and Barro was taken over by the Southern Pacific and used as a freight spur into the 1980s.

The freight service to Mare Island Naval Shipyard remained as a subsidiary of the Sacramento Northern Railway until taken over by the Navy Department in 1956.

[7]: 3–10 The railroad's former car barn located at Sixth Street and Soscol Avenue in Napa, built in 1907, is still extant.