Lempuyangan Station has eleven train tracks. Originally only line 4 was a straight track. After the construction of the Surakarta–Yogyakarta
double track section was completed on 8 January 2007, track 3 was also used as a straight track. To the north of track 5 is a spur to the Yogyakarta Warehousing and Logistics Center (formerly the NIS
roundhouse) and Yogyakarta
railway workshop which is the largest train workshop in Java. The station has been equipped with signages, track directions accompanied by distance traveled, and screens to monitor train departures and arrivals in real time. In 2009, the station underwent overall repairs by adding a new building east of the old building. In mid-2017, the station area underwent another renovation. The An-Nuur Mosque, located west of the station building, was opened to the general public, while the prayer room located to the east is only used for passengers who have boarded or have not yet left. Expansion was also carried out in the parking lot and the extension of the station canopy roof. In 2018–2019, the An-Nuur Mosque was demolished to make other facilities. 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). Regarding the project to upgrade the train's electrical signaling system at the station, a new electric system produced by Len Industri as of April 2021 has been installed which will replace the old system produced by
Siemens. It has been active since September 2021. == Services ==