The Bayshore Cutoff was completed in 1907, running through terrain that required extensive grading, fill, and bridge construction along the San Francisco Bay shoreline. The route bypassed the steeper inland routing through the peninsula's hills, providing a faster, more level alignment for both freight and passenger service. The line passed through the industrial areas of southeastern San Francisco and the bayside communities of Brisbane, South San Francisco, and San Bruno, connecting at its southern end with the existing mainline that continued down the peninsula to San Jose.

At the San Francisco end, the Bayshore Yard and Roundhouse served as major maintenance and staging facilities for Southern Pacific's peninsula operations. The roundhouse, where locomotives were serviced and turned, became a landmark of the industrial waterfront. The yard handled freight switching and car storage for the southern approach to San Francisco. As diesel locomotives replaced steam and freight operations shifted, the facilities' importance diminished, but the corridor itself remained vital as the backbone of commuter rail service on the peninsula.

Today the Bayshore Cutoff carries Caltrain service between San Francisco's 4th and King Street station and the peninsula suburbs, one of the busiest commuter rail corridors in Northern California. The route passes through neighborhoods that have transitioned from heavy industry to a mix of biotech campuses, residential development, and surviving industrial operations. The electrification of Caltrain, completed in recent years, brought a new generation of electric multiple-unit trains to the corridor that Southern Pacific's steam engineers would not recognize. But the route is the same one they laid out in 1907, when seven million dollars could build a railroad along the bay.