La Crosse has a municipal airport located on French Island, a nearby suburb to the north. Flights often arrive from Chicago, Milwaukee, and Minneapolis.
A full service Amtrak Station is located on the North Side providing daily service on the Empire Builder route.
Two Greyhound Bus stations are located in La Crosse. One is connected to the Amtrak Station on the citie's North Side, and the other is located near the University of La Crosse on the south side.