Nearest major airport to La Crosse County, Wisconsin: The closest major airport to La Crosse County, Wisconsin is La Crosse Municipal Airport (LSE / KLSE). This airport is in La Crosse, Wisconsin and is 7 miles from the center of La Crosse County, WI. If you're looking for domestic flights to LSE, check the airlines that fly to LSE. Search for direct flights from your hometown and find hotels near La Crosse County, WI, or scroll down for more international airports or domestic airports.