During the 1863 Gettysburg Campaign, Archer's health continued to deteriorate as a result of long marches in the summer heat and humidity. His brigade was now part of the division of Maj. Gen. Henry Heth. Arriving at Gettysburg on July 1, Archer's troops were engaged with Federal cavalry under John Buford for over two hours, before being counterattacked by rapidly arriving Union infantry, including the famed Iron Brigade. Archer's men were likely those who killed Union commander Maj. Gen. John F. Reynolds (the exact cause of Reynolds' death is controversial), but were quickly pushed back across Willoughby Run, where the exhausted Archer took cover in a thicket. A Union soldier, Private Patrick Maloney of the 2nd Wisconsin, seized Archer and escorted him behind enemy lines, where he briefly met an old colleague, Union Maj. Gen. Abner Doubleday. Archer became the first general officer to be taken captive from the Army of Northern Virginia since General Lee assumed command. Birkett D. Fry assumed command of Archer's Brigade and led it during Pickett's Charge, while Archer and his younger brother and aide-de-camp Robert Harris Archer (1820–1878) were sent to Fort Delaware for prisoner processing.