It was intended as part of the scheme to provide an adequate transport system during the 1972 Summer Olympics held in Munich by connecting the pre-existing suburban rail services in the west and east of the city via a new tunnel section from Hauptbahnhof to Ostbahnhof.

Operational requirements have changed several times, particularly due to line extensions, resulting in random numbering in the east.

There are also occasional additional trains on the western section of the S4 and on the S1 between Freising and Munich during the peak hour, which do not continue past the Hauptbahnhof (not run through the trunk line tunnel).

Additional regional lines make calls at stations also served by the S-Bahn but provide an effective express functionality for MVV passengers.

On 22 May 1938, the first tunnel, which was part of the north–south route, was started in the Lindwurmstraße, between the present-day underground stations Sendlinger Tor and Goetheplatz.

In the speech of Julius Dorpmüller, the general director of Deutsche Reichsbahn, the project was called "S-Bahn" for the first time.

However, the floor height of trains used then and now is at approximately 1 metre (3 ft 3 in), which makes boarding difficult for people with wheelchairs or prams.

Tunnel stations and platforms updated recently where no freight trains run do feature a height of 96 centimetres (3 ft 2 in), however.

On 28 May 1972, the Munich S-Bahn network was finally put into service with 360 kilometres (220 mi) of tracks and 101 trains of the ET 420 series.

The route S10 to Wolfratshausen (today S7) was operated with conventional push-pull trains from the southern wing of Munich Central Station.

It was electrified later and connected to the core route after the construction of a 260-metre (850 ft) tunnel crossing the large number of mainline rail tracks leading to Munich Central Station.

In August 1998, the federal government, the Free State of Bavaria and Deutsche Bahn decided on a 266-million-euro package to introduce this ten-minute headway on several lines.

On 15 December 2013, the S 27 from the main station to Deisenhofen was discontinued, the trips are taken by the half-hourly Meridian trains of the Bayerische Regiobahn, which are extended in the rush hour via Holzkirchen and the Mangfalltalbahn to Rosenheim.

These are 15 units taken over from the S-Bahn Stuttgart, but due to the lack of regular train traffic, they can not run on the main line during rush hours.

[10] A more powerful HVAC system, new passenger information displays showing occupancy, station stops and nearest exits on the platform, and free Wi-Fi will be fitted.

[9] The European Investment Bank and HypoVereinsbank, a subsidiary of UniCredit, provided credit of more than €2 billion for the order, with LHI Leasing selected as the lessor.

In 1972, during the Olympic Games, a consist made up of 15 Silberlinge cars and a DB Class 140 locomotive at the middle was used to haul trains on the S25 between the Ostbahnhof and the Olympiastadion stations.

[13] In 1989, the Dubbeldeksmaterieel [nl] (DDM-1) double decker carriages used by Nederlandse Spoorwegen in the Netherlands were briefly trialled on the then S4 between Geltendorf and Ebersberg.

[14] Nearly all lines use the core route through the city centre in the underground, creating a bottle-neck responsible for long and increasingly frequent delays from even the smallest disruptions.

After years of discussions and studies into different route propositions, a second tunnel through the city centre has been already approved with the funding of €3.85 billion and the completion date of 2028–2032.

With focus on express service and shorter travel time, the second tunnel will bypass six current stations between Laim and Ostbahnhof.

The residents have grave concern about tunnelling and earth extraction impacting their housing and disrupting their daily lives.

This route would use part of Münchner Nordring (Munich North Ring) currently used by the freight trains and as railway bypass.

The advantage of using the Nordring is numerous as compared to Südring (South Ring – proposed as an assumedly weak alternative to second trunk line): The discussion of S-Bahn-Nordring is ongoing with no tentative date of construction and completion as well as cost estimate.

Michael Piazolo, a Bavarian state parliament representative, commissioned a study for a potential Münchner Ringbahn.

[21] The proposal of building the circular railway similar to Berlin Ringbahn has recently gained more traction with the city government and the state parliament.

The close proximity of Nymphenburg Palace and the west–east lines at Donnersbergerbrücke station would require the construction of tunnels between south of Heimeranplatz and Olympiakreuz.

Most of the Ringbahn would use the existing railway lines with seven S-Bahn stations (Heimeranplatz, Donnersbergerbrücke, Johanneskirchen, Englschalking, Daglfing, Leuchtenbergring, and Ostbahnhof) currently in use.

That could potentially shorten the travel time from the Hauptbahnhof on the west side, bypassing the current S2 with numerous stops along the line.

[23] In 2009, a Nordtunnel was proposed by Vieregg-Rössler as a further extension, which connects the main railway station with the Kunstareal (with the three Pinakotheken) Nordring, football stadium, Garching, airport).