| Direction | Numbers | Odd/Even | Days of Operation |
| Northbound Local Tamien or San Jose-San Francisco | 101-173 | odd | Weekdays |
| Southbound Local San Francisco-San Jose or Tamien | 102-176 | even | Weekdays |
| Northbound Limited San Jose-San Francisco | 401-429 | odd | Weekdays |
| Southbound Limited San Francisco-San Jose | 404-428 | even | Weekdays |
| Northbound Express San Jose-San Francisco | 503-527 | odd | Weekdays |
| Southbound Express San Francisco-San Jose | 502-528 | even | Weekdays |
| Northbound Local Tamien or San Jose-San Francisco | 601-665 | odd | Weekends |
| Southbound Local San Francisco-San Jose or Tamien | 602-668 | even | Weekends |
| Northbound South County Connector Gilroy-San Jose | 805-811 | odd | Weekdays |
| Southbound South County Connector San Jose-Gilroy | 814-822 | even | Weekdays |
