Johor Bahru Sentral also is the southern terminus of KTM Intercity train services to Gemas and Pulau Sebang/Tampin via Ekspres Selatan or Tumpat via Ekspres Rakyat Timuran. KTM Intercity via Shuttle Tebrau also serves the Woodlands Train Checkpoint in Singapore across the Johor–Singapore Causeway. However, an electric train connection at Gemas is required for passenger to KL Sentral, Butterworth and Padang Besar.

Johor Bahru Sentral serves as the Malaysian immigration checkpoint for southbound rail passengers towards Woodlands. Northbound rail passengers from Woodlands are processed by Malaysian immigration and customs officers at Woodlands Train Checkpoint prior to boarding.