Today, the SD&AE operates approximately 108 miles (174 km) of the original SD&A system, across four segments:[1] The San Diego and Arizona Eastern Railway traces its origins back to December 14, 1906, when entrepreneur John D. Spreckels announced he would form the San Diego and Arizona (SD&A) Railway and build a railroad to provide San Diego with a direct rail link to the east by connecting with the Southern Pacific (SP) lines in El Centro, California.

As part of the agreement, the SD&A is ordered to form the Tijuana and Tecate Railway, which will construct and hold a 99-year lease on the 44-mile (70.81 km) Mexican rail segment.

In Mexico, revolutionaries mount several attacks on SD&A construction crews to conscript soldiers, take supplies, and cut telephone wires.

On the U.S. side, the federal government seized control of all railroads in 1917 and stopped construction in an effort to conserve resources amid World War I.

Rains washed away large amounts of trackage east of San Diego in 1926, 1927 and 1929, leading to financial troubles for the railroad.

[5] The San Diego Metropolitan Transit Development Board (MTDB) stepped in and offered to buy the SD&AE for $18.1 million if SP fully repaired the line.