Constructed from 1992 to 1997, Woodlands Train Checkpoint was opened on 1 August 1998 as the Singapore border control facility for rail passengers.

At that time there were no boarding facilities, as northbound passengers heading towards Malaysia were required to clear Malaysia's customs and immigration at Tanjong Pagar railway station, and northbound trains stopped at Woodlands Train Checkpoint for Singapore exit immigration checks only.

[3] The diesel powered Eastern and Oriental Express (E&O) has its southern terminus at Woodlands Train Checkpoint.

Until 1998, both Malaysia and Singapore had their customs and immigration facilities for rail passengers at Tanjong Pagar railway station.

Singapore decided to relocate its customs and immigration facilities to Woodlands despite Malaysia's unwillingness to vacate the Tanjong Pagar railway station according to the Malaysia–Singapore Points of Agreement of 1990.

KTM together with Malaysian customs and immigration relocating their operations to Woodlands Train Checkpoint on 1 July 2011 in agreement with Singapore.