It is located below Isartorplatz and the Thierschstraße/Zweibrückenstraße intersection in Munich and is named after the nearby Isartor city gate.

Because the S-Bahn trunk line passes under the Isar between the stations of Isartor and Rosenheimerplatz just to the east of the station, both tubes are fitted with flood gates so that the tunnel can be sealed watertight, so that in the event of flooding of the Isar the stations lying to the west are not also flooded.

Transfer facilities exist to tram lines 16 and 18[5] and to the bus route 132.

In 2007, the station was used daily (Mon-Fri) by 45,900 passengers, entering, exiting and transferring.

Isartor is also one of only two stations with their island platforms not arranged in Spanish solution, the other one is München Rosenheimer Platz.