Malaysian and Thai immigration, customs and quarantine checkpoints are also co-located within this station specifically for cross-border train passengers.

Padang Besar railway station also has a freight yard that serves as a dry port for the northern part of Malaysia and Indonesia–Malaysia–Thailand Growth Triangle.

The station can be accessed by road which is linked to Federal Route 7 just outside Padang Besar town.

KTM has introduced a seasonal Ekspres Sawadee between Kuala Lumpur and Hat Yai in October 2022, where passengers disembark at the station to go through cross-border formalities before reboarding the train for the onward journey, similar to the practice for the previous International Express and Ekspres Semenanjung.

The facilities for each country operate from separate counters inside the railway station building at the platform level.