Altamont Commuter Express operates with zone fares, with a fare range between $4.25 (within Santa Clara County) and $14.50 (between San Jose and Stockton). Trains only operate in the peak direction of travel (from Stockton mornings, from San Jose afternoons and evenings), with four trips per way:
- Stockton departures: 4:20am, 5:35am, 6:40am, 7:05am
- San Jose departures: 3:35pm, 4:35pm, 5:35pm, 6:38pm
As recent as early 2018, ACE is proposing to:
- Expand its service span to introduce Saturday service, with two trains to San Jose mornings and two return trips to Stockton afternoons.
- Mount new service linking Manteca, Modesto, and Merced, with intermediate stops in between to provide additional service to the Central Valley in preparation for California High Speed Rail.
Since March 2020, only two trains per way operate on weekdays: the 4:20am and 5:35am trips from Stockton, and 3:35pm and 5:35pm trips from San Jose.