The Bayshore Cutoff (originally the Southern Pacific Bay Shore Cut-Off) is the rail line between San Francisco and San Bruno along the eastern shore (San Francisco Bay side) of the San Francisco Peninsula. It was completed by Southern Pacific (SP) in 1907 at a cost of $7 million (equivalent to $242 million adjusted for inflation), and included five tunnels, four of which are still used by Caltrain, the successor to Southern Pacific's Peninsula Commute service. Fill from the five tunnels was used to build the Visitacion or Bayshore Yard, the main SP classification yard near the city of Brisbane. The Del Monte was similarly rerouted over the line at some point in its operational history.

The original alignment of the Coast Line completed in 1863 took it around the western side of San Bruno Mountain, through Colma and Daly City. Rail traffic along the original route needed helper engines for grades and curves along a route nearly 13 miles (21 km) long. The Bayshore Cutoff reduced the distance to 10.5 miles (16.9 km) with a maximum grade of 0.3 percent.

Once the Bayshore Cutoff was completed, and main line traffic was shifted to it, the former route was renamed the Ocean View Branch line. It was used to carry coffins to Colma; it was severed in the 1940s, but a few miles at the south end was still in SP's 1996 timetable. In the late 1980s BART purchased the right-of-way of the Ocean View line for the San Francisco International Airport extension south from Daly City.

Bayshore Cutoff Tunnel 5, at Sierra Point, was abandoned when the easternmost tip of the point was leveled during construction of the Bayshore Freeway in 1955–56, and the line was rerouted through the leveled section as well. The rail yard was in operation until the 1970s, and the site is currently being considered for redevelopment for light industrial/retail use as part of the Brisbane Baylands development project.

The original route between San Francisco and San Bruno was laid by the San Francisco and San Jose Railroad (SF&SJ), one of the companies that later was absorbed into the Southern Pacific (SP). From the station in San Francisco at Mariposa and 18th, tracks were laid generally bearing west-southwest through the Mission District close to the present-day route of San Jose Avenue.

Southern Pacific took over the Peninsula Corridor in 1870 from the SF&SJ and began operating the Peninsula Commute between San Francisco and San Jose. Surveys were conducted for an alternate route east of San Bruno Mountain as early as 1878 and in 1894, it was revealed that SP had secretly purchased a more direct route along the shoreline of San Francisco Bay through an agent, Alfred E. Davis, who had previously been the manager to James G. Fair, the financier of the South Pacific Coast Railroad, a narrow-gauge railroad from Oakland to Santa Cruz. The Bay Shore line to South San Francisco opened from the south in May 1892, which would be integrated into the final alignment. By 1900, the Bayshore Cutoff route, including five tunnels, had been designed and plans were announced to start work "within a few weeks". The San Francisco Board of Supervisors attempted to compel SP to start using the Bayshore route by passing an ordinance in 1900 directing the Board of Public Works (BPW) to tear up the existing tracks. SP was granted an injunction to prevent that action, but BPW Commissioner Maguire planned to bring witnesses "to testify that the clanging of bells, shrieks of whistles, etc., interferes with the comfort and peace of the surrounding residents."

SP announced firm plans to build the Bayshore Cutoff and double-track the line in late 1901. President E. H. Harriman reiterated SP's plans to construct the Cutoff in mid-1902, predicting completion within the calendar year. Double-tracking from Burlingame south to San Jose was announced as well, and completed by 1903. In conjunction with the Dumbarton Cutoff, the Bayshore Cutoff was designed to facilitate transcontinental rail service into San Francisco. Instead of being a remote spur terminal, San Francisco would become "practically the same as a main line station" with the completion of the two new cutoffs, and transcontinental freight could then be loaded directly on trains without having to be ferried across the Bay.

The San Jose-based Evening News touted the benefits of the Cutoff, saying the fifteen minute savings in travel time combined with a more temperate climate would naturally lead to increased population in San Jose: "The warmer, drier and more even climatic conditions make [San Jose] far preferable for residence to a place where the men feel the need of an overcoat in the evening of the warmest days, and where the ladies scarcely know what it is to dress in light clothing and walk out in the evening." In 1903, the route of the Bayshore Cutoff was adjusted slightly; the original route called for tracks along Islais and Tulare streets, which due to their narrow width, would have closed those streets to any other traffic. Over a one-year period, Joseph B. Coryell acted as agent for SP to purchase properties bordering Islais Creek to allow the rerouting of the line.