Built by the Japanese Imperial Army during the Japanese occupation of Singapore in World War II, the shrine was destroyed directly before British forces re-occupied Singapore.

Major Yasuji Tamura, the commander of the Japanese 5th Division's Engineers Regiment and the man in-charge of the design and the construction of the Syonan Jinja, had envisioned for the shrine in Singapore to be best Shinto shrine in the whole of the southern areas of Asia that has come under Japanese occupation.

[3] Just before the Japanese officially surrendered on 15 August 1945, they decided to destroy and burn the shrine to the ground in fear of its desecration by the returning British colonial forces.

[3] The ruins of Syonan Jinja – now down to a few remaining support structures and broken pieces and chunks – can still be found in the dense tropical forest of the Central Catchment Nature Reserve (CCNR), in which includes the MacRitchie Reservoir.

[3] However, the historical site remains inaccessible to the public due to the strong current deep stream and the presence of wild animals.