The existing route, originally built by the Green Bay and Lake Pepin Railroad, linking Green Bay, Wisconsin, and East Winona, Wisconsin, formed the bulk of the new railroad.

The GBW established in 1929 the Western Refrigerator Line Company (WRX) to operate a 500-car fleet of reefers.

The Green Bay & Western and the Fox River Valley Railroad were merged into a new Wisconsin Central subsidiary, the Fox Valley and Western Railroad August 27, 1993.

Wisconsin Central was, in turn, purchased by Canadian National railway in 2001.

The GBW prospered from 1892 when a train ferry was introduced across Lake Michigan from Kewaunee eliminating transhipment and bypassing the congested Chicago area.