He served with the 69th New York Infantry Regiment, from its days as a militia unit and into its incorporation into the Union Army at the start of the war, and was one of its senior officers at the First Battle of Bull Run.

He did encounter resistance from city officials wanting him to remain uninvolved, but by mid-June he had reported to his superior officer, provost marshal general Colonel James Fry, that conscription efforts were "nearing completion without serious incident".

Returning to active duty, he assumed command of the Irish Brigade in December 1863, shortly after Corcoran's death, and was present at the Battle of Spotsylvania and the Petersburg and Appomattox Campaigns.

The veterans of the Irish Brigade were honorably discharged and mustered out three months later; Nugent remained in the regular US Army for the next twenty years and was a formidable "Indian fighter" during the Great Plains Wars with the 13th and 24th Infantry Regiments.

In 1879, he retired at the rank of major and resided in New York, where he was involved in the Grand Army of the Republic and the War Veterans' Association of the 7th Regiment, and an honorary member of The Old Guard.