Tomah is a regional transportation hub because of its location "where the 'I' divides." For westbound travel, Interstate 94 and Interstate 90 share a roadway from Madison, Wisconsin to Tomah, where they diverge. Interstate 90 continues west to La Crosse, Wisconsin while Interstate 94 heads north to Eau Claire, Wisconsin and the Twin Cities.
Tomah is also served by an Amtrak Station on the Empire Builder route.