Governor Randall appointed 41-year-old S. Park Coon colonel of the new regiment—Coon was a native of New York, had served as Wisconsin's 2nd Attorney General, and was an influential Milwaukee County Democrat.

[3]: 438  Although President Lincoln's original request was for three-month volunteers, by June the need had become apparent for longer enlistments, and the 2nd Wisconsin was mustered as a three-year regiment.

At the battle some of the men wore state militia grey uniforms, causing the 2nd Wisconsin to receive friendly fire from Union troops mistaking them for Confederates.

The appointment of O'Connor, married to a Southern woman and an outspoken Democrat, was met with sharp criticism in Wisconsin's media, particularly in the Republican newspapers.

During the subsequent Maryland Campaign, the 2nd Wisconsin attacked Turner's Gap during the Battle of South Mountain, and then again took high casualties in the Cornfield at Antietam.

Perhaps the regiment's finest hour came at Gettysburg, where it lost 77% of its strength (233 casualties out of 302 effectives) in stubborn fighting on McPherson's Ridge during the Iron Brigade's lengthy action on July 1, 1863.

With the regiment's original three-year enlistments expiring on June 11, 1864, those who chose not to re-enlist were sent back to Madison, with the final company mustering out on July 2, 1864.

Newer recruits and re-enlisted veterans were restructured into a battalion of two companies, first under the command of Captain Dennis B. Dailey, then under Lt. Albert T. Morgan, and finally Lt. Henry Naegly.