Railroad operations began in 1879 with the construction of the Sonoma Valley Railroad. This line, built from the edge of the bay to Sonoma in 1878, reached Glen Ellen about a year later. Subsequently, it was extended to Ignacio in Marin County for connection with the San Francisco and North Pacific Railway. The railroad was built by local interests but Peter Donahue, the builder of the San Francisco and North Pacific, seeing the advantage of the line took control in the 1880's.

The original station and yards were in the northwest corner of Sonoma Plaza. The line was narrow gauge but was converted to standard gauge in 1890. When the conversion was made, the route through Sonoma was moved to the north through purchase of right-of-way by local citizens who, although wanting a railroad, did not think that the Plaza was the best location.

The line carried passengers and freight including basalt cobblestones to pave for San Francisco streets.

Adapted from the NRHP nomination.