Owing largely to high bounties paid out and a smaller pool of available men of age since the war was in its later days, the unit suffered heavy desertion rates - the highest of any New Jersey infantry regiment.
Due to the haphazard way the unit was organized, many officers served in their duty in the field long before they were officially mustered in.
Although the unit as it existed at the time was present at the Battle of Hatcher's Run near Dabney's Mills on February 5–7, 1865, the 40th New Jersey participated in their first and last battle on April 2 at Petersburg, where it participated in the final Union army assaults on Confederate entrenchments.
Private Frank E. Fesq of Company A captured the battle flag of the 18th North Carolina Infantry during the assault, earning him the Medal of Honor.
The regiment remained in occupation duty after the Confederate surrender, then was mustered out at Hall's Hill, Virginia, on July 13, 1865.