Today, Caltrain and the Union Pacific Railroad continue to operate trains over part of the company's original route.

[2] The company reorganized on October 29, 1853, just before the expiration of the construction permit, and US$2,000,000 (equivalent to $73,250,000 in 2023) of stock was drawn up for sale, but an untimely downturn in the economy meant no investors were forthcoming.

[2] With the Civil War consuming men and material, iron suppliers were only willing to deal with cash, not credit, and several members of the SF&SJ board of directors, including Peter Donahue, Henry Newhall, and Charles B. Polhemus used their personal influence and effort to secure material for the railroad.

[2] Construction wage scale on railroads, at $27 per month with board, was substantially lower than that of common laborers in the mines or in the cities at the time.

[1][5] Hiring Chinese in the early and mid 1860s was not as controversial as expected and garnered few notices, as it was a short period of time of less hostile anti-Chinese sentiments.

[10] Four months later, the railroad was opened for excursion service between San Francisco and Menlo Park on October 17, 1863.

The second train departed at 11:15 AM after adding several cattle cars to accommodate the estimated 700–800 passengers; that second train stopped briefly in San Mateo to take on fuel and water, and proceeded past waiting passengers at Redwood City and Mountain View, arriving in Santa Clara by 12:45 PM.

[12] In February 1864, the SF&SJ advertised regular passenger service on four trains per day, with the trip scheduled to take two hours, twenty minutes each way.

[14] With the decline of placer mining, the completion of the railroad enabled the ascendancy of agriculture as a major new industry in California.

[4] With the exception of the single 0-4-0 switcher, number 8, all SF&SJ locomotives were the American 4-4-0 type typical of that era.

[18] The first full-sized steam locomotive produced in the state of California was built for the SF&SJ by the Union Iron Works in San Francisco.

[18] In 1854, Charles B. Polhemus purchased the land which would later become Central Park (San Mateo)[20] he built a mansion on the grounds.

In 1869, Polhemus bought Rancho San Miguelito de Trinidad and sold it in 1872 to his business partner, Henry Mayo Newhall.

Polhemus bought Rancho El Piojo at a foreclosure sale, and sold it in 1871 to his business partner, Henry Mayo Newhall.