When the Manggarai-Jakarta Kota cross line was still below (at-grade with ground level), this station did not yet exist.

In February 1988, the Manggarai–Jakarta Kota elevated railway project was held which cost Rp.

[3] On June 5, 1992, President Soeharto along with Mrs. Tien Soeharto and other government officials inaugurated this elevated train line by taking the executive class Rheostatic electric multiple unit (KRL) from Gambir Station to Jakarta Kota Station.

[3][4][5] The Jayakarta Station building is in a modern style, with a touch of fanta pink panels which are still maintained to this day and have never been painted, only the platform poles have been changed to crimson.

The reason is that this elevated train line will descend and tread to the ground and end at Jakarta Kota Station.