[3][4] The new Woodlands Checkpoint, built partially on reclaimed land, was opened in 1999 to accommodate the increasing traffic flow and the soot which had enveloped the old customs complex over the years.

Southbound rail passengers clear Malaysian exit controls at JB Sentral, and Singapore immigration and customs on arrival at Woodlands Train Checkpoint.

This was due to the fact that Singapore and the rest of Peninsular Malaysia had either been under a single sovereign control (in the form of British colonial administration, Straits Settlements, and Malayan Union and Japanese occupation during World War II in Asia) or enjoined in a single political entity (Federation of Malaysia).

During these periods of singular external control, the security of Singapore's side of the Causeway had been nominally managed by the local police authorities.

[9][10] Generally people at both sides of the causeway could travel between Singapore and Johor, ergo Peninsular Malaysia freely.

[11] Since the independence of Singapore, there have been several physical replacements of the Woodlands Checkpoint complex to accommodate the growing traffic between the two countries, but they have largely located within the same area.

The process of establishing diplomatic recognitions between Singapore and Indonesia had left Malaysian politicians feeling uneasy.

Due to new immigration laws, a checkpoint was established at Woodlands to check on all foreigners, except those who held Malaysian identity cards or having special visa arrangements entering Singapore effective 2 August 1966.

[24] The opening of the checkpoint also signalled the implementation of the Exit Control Scheme, which was to prevent visitors to the nation from overstaying.

[32] On 30 March 2017, authorities announced that the Old Woodlands Town Centre (OWTC) and two privately-owned blocks were compulsorily acquired by the government, in order for the land to be converted into an extension of the 1999 checkpoint.