When the Civil War began, Perrin entered the Confederate service as a captain in the 14th South Carolina Infantry Regiment that was attached to Brigadier-General Maxcy Gregg's brigade of the famous "Light Division" of Major-General A.P. Hill.
Perrin saw service with Gregg's Brigade through all of its major battles, including the Seven Days, Cedar Mountain, Battle of Second Manassas, Antietam, and Fredericksburg. When Gregg's successor, Samuel McGowan, was wounded at Chancellorsville, Perrin took command of the brigade and led it at the subsequent Battle of Gettysburg in the division of Major General William D. Pender in Hill's new Third Corps. At Gettysburg, on July 1, 1863, Perrin's Brigade was involved in the Confederate attack that captured Seminary Ridge. On September 10, 1863, Perrin was promoted to the rank of brigadier-general. Upon the return of McGowan, Perrin was transferred to command the Alabama brigade previously led by Brigadier-General Cadmus Wilcox in the division of Major-General Richard H. Anderson (Wilcox had been appointed to command the division of Pender, who had died from a wound received at Gettysburg).
Perrin was conspicuously brave at the Battle of the Wilderness in May 1864. In the next battle, Spotsylvania Court House, he declared "I shall come out of this fight a live major general or a dead brigadier." When the "Mule Shoe" (or "Bloody Angle") was overrun and most of Major-General Allegheny Johnson's division was captured on May 12, 1864, units from the Third Corps—including Perrin's Brigade—were called in to help. Leading his troops in a spirited counterattack through a very heavy fire, with his sword in hand, Perrin was riddled with bullets and died instantly, shot seven times. He is buried in the Confederate Cemetery in Fredericksburg, Virginia.
