The earliest attempts to implement an electrified suburban rail system in Warsaw were made in 1936–37, when the Warsaw Railway Junction and surrounding railway lines were electrified to the national standard of 3 kV DC and high platform electric multiple units were introduced (which later came to be designated PKP class EW51).

The Warsaw SKM in its current form was proposed in late-2002, stipulating to use the existing infrastructure of the Warsaw Railway Junction, especially the cross city line with its over 2 km long tunnel running under the city center and conveniently located underground station, as a cheap substitute for a badly needed second metro line whose construction did not start until 2010.

In order to implement this the then-Mayor of Warsaw Lech Kaczyński established in 2004 the municipally-owned company Szybka Kolej Miejska Sp.

As such the company is notably completely independent from the national rail operator PKP Group, unlike Koleje Mazowieckie established by the Masovian Voivodeship at around the same time.

The new service failed to deliver on its promise to serve as a viable replacement due to the poor state of the rail infrastructure.

Additionally, while the integrated fare system of the Warsaw Transit Authority offered a large convenience the modern look and relative cleanness of the rolling stock sharply contrasted with the standard found in the Polish railroad; during rush hours most of the slots on the tracks were taken up by regional traffic and the new EMUs suffered from the same technical problems as the ones they were based on.

Due to the initial low popularity of the line the original concept was somewhat altered in 2006 with the line extended outside the administrative borders of the city through the Ursus district into the town of Pruszków to the west and diverted to the district of the Wesoła and the town of Sulejówek to the east, turning the service into a suburban commuter network which allowed people in the metropolitan area to quickly reach the city center and conveniently transfer within the city's public transit system.

The popularity of the trains was also instrumental in the city negotiating a deal with the Masovian Voivodeship to have Koleje Mazowieckie honor long term tickets of the Warsaw Transit Authority, first along the route of the SKM and eventually within the entire area served by the city's public transit system.

In June 2012 the line was extended from Warszawa Zachodnia through the Służewiec office district and a newly opened rail tunnel to an underground station at the Warsaw Chopin Airport.

The route assumed its current form on 12 March 2023 due to modernization works at Warszawa Zachodnia station and the Warsaw Cross-City Line.

It connects city of Piaseczno in south-west with Wieliszew in north-east, running through Warsaw and crossing the Vistula by northern railway bridge.