It is 1 kilometre (0.62 mi) east of Yogyakarta Station, 114 metres (374 ft) above sea level.

Lempuyangan Station was inaugurated on 2 March 1872 by the Dutch East Indies private railway company, Nederlandsch-Indische Spoorweg Maatschappij (NIS) as the end point of the Semarang–Solo–Yogyakarta cross-rail line and is the first and oldest train station in Yogyakarta.

The station has been equipped with signages, track directions accompanied by distance traveled, and screens to monitor train departures and arrivals in real time.

Expansion was also carried out in the parking lot and the extension of the station canopy roof.

Since March 2020, the vacant land located on the west side of Lempuyangan Station has been developed into a RailExpress warehouse (now KAI Logistik Ekspres).