Previously, Majdal railway station, built by the British forces during World War I, has existed at the site, and since 1920, the station served regular passenger trains between El Kantara, Egypt and Haifa.

During 1948 Arab-Israeli War, the connection to Gaza Strip and Egypt was severed, but freight service on the Lod–Ashkelon railway continued.

This new line was inaugurated on 4 August 2013 and significantly shortened the travel time from Ashdod and Ashkelon to Tel Aviv to 35 and 45 minutes respectively.

The railway line south of the station was extended to Beersheba beginning in 2006, which enabled rail service to the towns of Sderot, Ofakim and Netivot in the northern Negev.

The station complex also houses a large electric multiple unit train maintenance depot that was completed in 2021.