The line leaves the Bavarian capital of Munich to the north, running on the left (western) side of the Isar river through the city of Unterschleißheim to Freising, and then curves to the east and runs through Moosburg, where it crosses the Amper river, continuing to Landshut Hauptbahnhof (central station), north of the centre of Landshut, the capital of Lower Bavaria.

It then curves to the north and, after crossing the watershed between the Danube and the Isar at Kläham, slowly descends and ends in the city of Regensburg, the capital of Upper Palatinate.

In the summer of 1870 construction started on a line from Neufahrn to Eggmühl and Obertraubling, considerably shortening the route between Landshut and Regensburg.

Between 1966 and 1972, the stations of Freising, Neufahrn, Lohhof, Feldmoching and Moosach and the halts of Pulling, Eching and Fasanerie were rebuilt with 76 cm high platforms and the tracks were adapted for the Munich S-Bahn.

In 1998 the western link to Munich Airport was opened as a two-track line which branches off north of Neufahrn at a flying junction.