A side platform adjacent to the station building serves track 1, whilst an island platform, accessed by a pedestrian subway, serves tracks 3 and 4.

Adjacent to the station is a seven track depot building, responsible for maintaining the snow clearance equipment used on the Bernina line.

[1][4][5] As of the December 2023 timetable change,[update] the following services stop at Pontresina:[6][7] The line from Samedan is electrified using the Rhaetian Railway's standard 11 kV AC, but the Bernina line uses its own 1000 V DC electrification, which introduces some complications into the operation of the station.

Tracks 1 and 2 are electrified at 11 kV AC and used by trains from Samedan terminating at Pontresina.

Tracks 4 to 7 are electrified at 1000 V DC and used by trains operating between St Moritz and Tirano over the Bernina line.