He assisted in routing a force of guerillas at La Hoya, fought at Huamantla, Puebla, and Atlixco, entered the city of Mexico, and was finally stationed at San Ángel until the close of the war.

He was mustered out of service with his company at Philadelphia on July 27, 1848, and the inhabitants of Schuylkill County, Pennsylvania, presented him with a commemorative silver and gold-plated sword.

[3] In 1861, following the outbreak of the Civil War, Nagle was commissioned as the colonel of the 6th Pennsylvania Infantry, a regiment with a three-month term of enlistment.

He was appointed brigadier general of volunteers on September 10, 1862, and at Antietam his brigade performed an important part in carrying what later became known as Burnside's Bridge, which, according to army commander George B. McClellan, saved the day.

[1] Nagle's appointment expired on March 4, 1863, but was renewed nine days later and he served with his brigade in Kentucky until May 9, when he resigned due to impaired health (he suffered from heart disease).

He subsequently commanded a brigade of emergency militia, and was mustered out on August 2, 1863, following the end of the Gettysburg Campaign and the retreat of Lee's army into Virginia.