The Green Bay and Western Railroad was formed in 1896 from the bankruptcy proceedings of the Green Bay, Winona & St Paul and the Kewaunee, Green Bay and Western. 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 Green Bay and Western acquired on August 1, 1906 a majority of shares/interest in the Ahnapee and Western Railway, and in 1929, the GBW established the Western Refrigerator Line Company (WRX) to operate a 500-car fleet of reefers.
Passenger traffic ceased in April 1949. The Line had carried 50,000 passengers yearly in the 1870s, 310,000 in 1915 but only 1,000 in 1947 having reverted to mixed trains.
The Green Bay and Western sold off the Ahnapee and Western Railway to Vernon M. Bushman and a group of private investors on May 31, 1947. The Itel Corporation purchased the Green Bay & Western in 1978. 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.