In 1995, San Joaquin County and seven cities along the route formed the San Joaquin Regional Rail Commission (SJRRC) to oversee the creation of the service.
In May 1997, the Altamont Commuter Express Joint Powers Authority (ACE JPA) was formed by the SJRRC, Santa Clara Valley Transportation Authority (VTA), and Alameda Congestion Management Agency (ACMA). That agreement formalized financial support, administrative processes, and governance for the rail service.
The operation is funded by a variety of state and federal sources, largely sales tax revenue collected by the three JPA signatories; farebox revenues account for about one-third of costs.