WSOR began operations in 1980 when the state acquired several Milwaukee Road branch lines and signed a 50-year agreement with the Wisconsin and Southern Railroad, organized by the FSC Corporation, which also owned the Upper Merion and Plymouth Railroad.
In August 1992, WSOR gained control of the Wisconsin and Calumet Railroad, which had been created in 1985 to replace the Chicago, Madison and Northern Railroad's operations on state-owned lines formerly part of the Milwaukee and Illinois Central Gulf Railroad.
The latter has since been abandoned except for a short stub at Madison.
WSOR thus gained access to Chicago (through trackage rights over Metra from Fox Lake), Janesville, Madison, and Prairie du Chien.
Further expansion came with a lease from the Union Pacific Railroad (UP) of Madison-area ex-C&NW trackage in 1996, and of an ex-Milwaukee Road line between Madison and Watertown from the Soo Line Railroad in 1998 (sold outright in 2003).
The most recent acquisition was north of Milwaukee in 2005, when the state purchased the ex-Milwaukee Road line between Saukville and Kiel, which Wisconsin Central Ltd. was going to abandon.
Soon thereafter, WSOR leased in part and bought in part an ex-C&NW line to Sheboygan from UP.

WSOR was named the 2009 Regional Railroad of the Year by Railway Age magazine.

On April 11, 2011, WSOR's president and chief executive officer (CEO), William Gardner, was charged with two felonies after he was accused of funneling more than $60,000 in illegal campaign contributions through WSOR employees during the 2010 Wisconsin gubernatorial election.
Gardner agreed to plead guilty to two felony counts.
Under a deal, prosecutors agreed not to seek jail time but instead would seek two years of probation.
In a statement, Gardner acknowledged his mistakes and said he took full responsibility.
The vast majority of the contributions were to Wisconsin Governor Scott Walker.

On November 29, 2011, it was announced that WSOR would be acquired by Watco Companies, with the deal to close on January 1, 2012.

In December 2012, the state of Wisconsin issued $17.1 million in financial aid to WSOR to rehabilitate 11 miles (18 km) of rail line between Plymouth and Kohler, which connects with existing WSOR tracks at Plymouth.
Service has begun as of 2015.

WSOR planned to operate a terminal railroad in Madison called the Madison Terminal Railway.
WSOR began operations in 1980 when the state acquired several Milwaukee Road branch lines and signed a 50-year agreement with the Wisconsin and Southern Railroad, organized by the FSC Corporation, which also owned the Upper Merion and Plymouth Railroad. In August 1992, WSOR gained control of the Wisconsin and Calumet Railroad, which had been created in 1985 to replace the Chicago, Madison and Northern Railroad's operations on state-owned lines formerly part of the Milwaukee and Illinois Central Gulf Railroad. The latter has since been abandoned except for a short stub at Madison. WSOR thus gained access to Chicago (through trackage rights over Metra from Fox Lake), Janesville, Madison, and Prairie du Chien. Further expansion came with a lease from the Union Pacific Railroad (UP) of Madison-area ex-C&NW trackage in 1996, and of an ex-Milwaukee Road line between Madison and Watertown from the Soo Line Railroad in 1998 (sold outright in 2003). The most recent acquisition was north of Milwaukee in 2005, when the state purchased the ex-Milwaukee Road line between Saukville and Kiel, which Wisconsin Central Ltd. was going to abandon. Soon thereafter, WSOR leased in part and bought in part an ex-C&NW line to Sheboygan from UP.
WSOR was named the 2009 Regional Railroad of the Year by Railway Age magazine.
On April 11, 2011, WSOR's president and chief executive officer (CEO), William Gardner, was charged with two felonies after he was accused of funneling more than $60,000 in illegal campaign contributions through WSOR employees during the 2010 Wisconsin gubernatorial election. Gardner agreed to plead guilty to two felony counts. Under a deal, prosecutors agreed not to seek jail time but instead would seek two years of probation. In a statement, Gardner acknowledged his mistakes and said he took full responsibility. The vast majority of the contributions were to Wisconsin Governor Scott Walker.
On November 29, 2011, it was announced that WSOR would be acquired by Watco Companies, with the deal to close on January 1, 2012.
In December 2012, the state of Wisconsin issued $17.1 million in financial aid to WSOR to rehabilitate 11 miles (18 km) of rail line between Plymouth and Kohler, which connects with existing WSOR tracks at Plymouth. Service has begun as of 2015.
WSOR planned to operate a terminal railroad in Madison called the Madison Terminal Railway.
Wisconsin and Southern Railroad