The station has two separated sections: underground subway section and above-ground JR section. In addition, Keihan Yamashina Station(京阪山科駅,Keihan Yamashina-eki) on the Keishin Line of Keihan Electric Railway is located just in front of the JR station. This article also covers the Keihan station.
The JR station has two island platforms with four tracks.
This station is an intermideate station on the "Biwako Line", but only the Tokaido Line for Maibara is informed as that common name, and the line for Kyoto and Osaka is as the "JR Kyoto Line". There are trains of the Biwako Line and the Kosei Line between this station and Kyoto.