This compared with about 75 minutes each way using the Jaffa–Jerusalem railway from Tel Aviv HaHagana to southern Jerusalem's Malha station, which unlike Jerusalem–Navon, is located relatively far from the city center.

A railway spur which opened on 31 March 2022 also enables direct service on the line between Jerusalem and Modi'in.

Eventually, trains from Jerusalem are expected to continue all the way to northern Israel as future phases of Israel Railways' electrification project are carried out along the Coastal Railway, with the long-term plan of trains originating from Jerusalem terminating at Karmiel by the mid 2020s.

Between 2000 and 2001, several alternatives were proposed:[5] Plans to build a line adjacent to Road 443 were discarded immediately, due to its being inside the West Bank.

This relatively long travel time, the non-central location of Malha station, and the low capacity of the line due to its eastern section consisting of only single-track meant that it continued to be one of the least-used lines in Israel Railways' network, despite connecting two large metropolises.

[9] Construction began in 2001 and was divided into multiple sections: Below is a breakdown of the tunnels, bridges and underpasses found along the route.

The section of the Eastern Railway between the airport and Lod station (which contains a major train maintenance depot) was also electrified.

Later, trains will be extended northwards towards Haifa and later to Karmiel as progress is made on electrifying the rest of the northern portion of the Coastal Railway.

The ministry further decided to indefinitely postpone implementing the plans for a future link from the railway to Modi'in (B2) east to Jerusalem.

[20] On December 2, 2008, the Israeli cabinet instructed Israel Railways to continue with the project despite the higher estimate and the Ministry of Finance to allocate the additional NIS 3 billion coverage necessary to proceed with construction.

Israel Railways published a tender for supervising the constructions of sections B and C, which stipulated that only companies with experience overseeing projects of NIS 1 billion or more could participate.

[10] A notable stumbling block, still unresolved as of January 2008, is the issue of where to put the excess dirt dug up in the tunnels.

[22] Additional dirt will be dumped in a new landfill on a site next to the Sha'ar HaGai interchange between Tel Aviv and Jerusalem.

[10] One of the main environmental issues with the project, and a source of opposition from green organizations, is the railway's passage through the Yitla Stream, a national park and Biblical location mentioned in the Book of Joshua.

[24] While Israel Railways and the Ministry of Finance claimed to oppose the longer combined tunnel proposal on financial and construction-time related reasons, Globes columnist Moshe Lichtman argued that the opposition was based on a combination of ego and the unwillingness, in principle, to change construction plans at the last minute.

[30] In addition, Israel Railways is due to introduce 60 new Siemens Desiro HC Double Decker EMUs by the end of 2021.

Similarly to the existing Bombardier TRAXX locomotives, these electric multiple units will travel at 160 km/h (100 mph) down the line.