The station is also served by limited Amtrak long-distance inter-city rail service, with the thrice-weekly round trip of the combined Sunset Limited/Texas Eagle.

When Amtrak took over intercity rail service in the United States in 1971, it continued serving Pomona with the Sunset Limited.

[7] The sbX Purple Line bus rapid transit route between Pomona–Downtown station and Ontario International Airport is expected to open in 2025.

[10][11] In 2020, it was discovered that multiple transients living in the nearby encampments had been regularly breaking into freight trains parked on the adjacent tracks.

[15] The Sunset Limited and the Texas Eagle both operate as a single combined train, with the eastbound train stopping at the station on Wednesday, Friday and Sunday at 10:40 p.m., and westbound trains stopping at the station on Monday, Wednesday and Friday at 4:00 a.m.[16][17] The Riverside Line follows the State Route 60 freeway corridor while the Sunset Limited and the Texas Eagle separates and follows the Alhambra Subdivision, owned by the Union Pacific Railroad.

The bus depot is located near the main station building, adjacent to the North platform, across from 1st and Commercial Streets.