The station is located on the Lötschberg line of the BLS AG, and is the junction point where the routes via the older Lötschberg tunnel and the more recent Lötschberg base tunnel diverge.

[1][5] As of the December 2024 timetable change,[update] the following services stop at Frutigen:[6][7] The station is also served by PostAuto bus service to Wengi, Reudlen and Reichenbach im Kandertal, Automobilverkehr Frutigen-Adelboden bus service to Kandergrund, Blausee, Mitholz and Kandersteg, and to Achseten and Adelboden.

[2][8][9] The northern portal of the Lötschberg base tunnel lies immediately to the south of the station.

Trains passing through the station are able to use either Lötschberg route, thanks to a grade-separated junction between the station and tunnel mouth.

[5] Whilst passenger trains on the base tunnel route can serve Frutigen station, only a few trains per day do so, with most stopping services operating via the old line.