Whitefish, Montana is the busiest station stop for the Amtrak Empire Builder in Montana based on ridership. The station had 68,223 boardings and alightings during Amtrak's 2006 fiscal year, an increase of 5,504 from FY2005. In addition to the Empire Builder, Amtrak Thruway Motorcoach also links the station to Kalispell and Missoula, Montana, USA. The station and parking lot are owned by the Stumptown Historical Society. BNSF Railway leases office space on the second floor of the station and owns the platform and track.

The Tudor Revival station building was listed on the National Register of Historic Places in 2002 and is known therein as the Great Northern Railway Passenger and Freight Depot and Division Office, or as the Whitefish Depot.