As the
American Civil War began in 1861, although his Quaker upbringing made Palmer abhor violence, his passionate abolitionism compelled him in keeping with the dictates of his conscience to enlist in the Pennsylvania volunteers. Palmer took a commission in the
Union Army. He organized the
Anderson Troop, an independent company of Pennsylvania cavalry, in the fall of 1861 and was elected its captain. Originally formed to act as a bodyguard for Brig. Gen.
Robert Anderson, it instead served as the headquarters cavalry for General
Don Carlos Buell, commanding the
Army of the Ohio. Impressed with the "elite scouts" that Palmer had assembled, Buell detailed Palmer and 12 of his men to go back to Pennsylvania to recruit more men to form a battalion around the Anderson Troop that would be known as the "1st Anderson Cavalry". In ten days of recruiting, however, Palmer received enough applications for enlistment to form a regiment, which was authorized as the
15th Pennsylvania Cavalry. He was appointed the regiment's colonel. Before Palmer was able to organize the regiment at Camp Alabama in
Carlisle, Pennsylvania, he and a portion of it were ordered on September 9 to help the
Army of the Potomac resist the
Confederates
invasion of Maryland. For nearly a week Palmer, accompanied by a
telegrapher, personally sought information of
Lee's movements every night in civilian clothing, and transmitted his findings to General
George B. McClellan via telegraph connections. Two days after the
Battle of Antietam, Palmer was captured while scouting at the personal direction of McClellan, seeking information on any preparations by Lee's army to cross the
Potomac River back into Virginia. He was on the Confederate side of the river, again garbed in civilian clothes and accompanied by a local blacksmith and a parson as his guides, attempting to recross to the Union side after midnight when he was captured by Confederate artillerymen sent to guard the dam he used for the crossing. When questioned, Palmer gave his name as "W.J. Peters," and claimed to be an engineer on an inspection trip. He was interrogated by General
William N. Pendleton, who thought he was a spy. He was detained and sent to
Richmond, Virginia, with a rambling note from Pendleton that was ignored. Palmer was incarcerated at the notorious
Castle Thunder prison on
Tobacco Row, Richmond where his true identity was never uncovered. Doubts about his identity were apparently reinforced by publication of a fictitious dispatch in the Philadelphia newspapers that purported that Palmer was in Washington, D.C., after scouting in Virginia. When he was freed after four months of confinement, he found that his guide, the Reverend J.J. Stine, had escaped but been arrested by Union authorities, accused of betraying him to the enemy. Rather than risk Palmer's life by publication of the circumstances in the Northern press, Stine had remained imprisoned in
Fort Delaware until Palmer's personal application to Secretary of War
Edwin Stanton resulted in his release. Palmer was set free in a prisoner exchange for a prominent Richmond citizen, recuperated two weeks, and rejoined his regiment in February 1863. During his period of imprisonment, the regiment had become mutinous because of a failure to have officers appointed and other enlistment inducements it felt had not been honored. 212 troopers faced court-martial and the possibility of going before a firing squad for refusing to fight in the
Battle of Stone's River. Palmer reorganized the regiment, personally appointed officers in whose abilities he had great trust, and had the charges against the confined soldiers dropped on the condition that they behaved going forward. The severely demoralized group of men rallied and distinguished themselves during the 1863
Tullahoma Campaign, the
Battle of Chickamauga, the capture of Brig. Gen.
Robert B. Vance's raiding cavalry and re-capture of 28 wagons of a foraging train in January 1864, and the
Franklin–Nashville Campaign. At Chickamauga, Palmer's regiment was detailed as headquarters guard for the
Army of the Cumberland with many troopers doled out to the various corps as couriers and scouts. When
Longstreet unexpectedly attacked the union right near
Rosecrans' headquarters, Palmer gathered all the men of his regiment available and prepared to counterattack with a saber charge. The Union right flank dissolved, however, and after attempting to rally the panicked infantry, his regiment crossed the battlefield in good order under Confederate artillery fire to protect the Union artillery. During the army's retreat to Chattanooga, the 15th Pennsylvania provided escort for the army's supply train. Not easily impressed, Major General
George H. Thomas (the "Rock of Chickamauga") recommended that Palmer receive a brigadier's star for his success at turning a highly demoralized group of men to an effective group of soldiers. Palmer was vigorous in pursuing Confederate General
John Bell Hood after the
Battle of Nashville in 1864. On March 9, 1865,
President Abraham Lincoln nominated Palmer for appointment to the brevet grade of
brigadier general of volunteers at the age of 28, with the U.S. Senate confirming the appointment on March 10, 1865. On March 16 he was promoted to command of the 1st Brigade of the Cavalry Division, District of East Tennessee, consisting of the 15th Pennsylvania, the
10th Michigan, and the
12th Ohio Cavalry Regiments. A month later he assumed command of the division after General
Alvan C. Gillem was promoted to command of the District of East Tennessee. Palmer was in the vanguard of Union General George
Stoneman's 1865 Raid into Virginia and North Carolina in the last two months of the Civil War. At Martinsville, Virginia on April 8, 1865, Palmer's cavalry defeated a Confederate force of Cavalry commanded by Colonel James Wheeler, the cousin of Confederate Cavalry commander Fighting Joe Wheeler. If Palmer had pushed on to Danville, only 20 miles to the north, he might very well have captured Jefferson Davis, who up till then had not left the capital of the Confederacy. Davis subsequently left the next day, upon receiving word of Lee's surrender. This was a little-known campaign immortalized in
The Band's epic, "
The Night They Drove Old Dixie Down". Palmer commanded the cavalry pursuit of
Jefferson Davis following the surrender by General
Joseph E. Johnston. Davis was followed through North Carolina, South Carolina, and Georgia and driven into the hands of General
James H. Wilson. During the pursuit, Palmer's former command overtook and captured wagons carrying millions of dollars of specie, bonds, securities, notes, and other Confederate assets, near
Covington, Georgia, that had been kept in the Bank of Macon (Georgia). Palmer was mustered out of the Union Army on June 21, 1865. General
George Henry Thomas wrote of Palmer: On February 24, 1894, Palmer was awarded the
Medal of Honor for his actions as colonel leading the 15th Pennsylvania Cavalry at
Red Hill, Alabama, January 14, 1865, where "with less than 200 men, [he] attacked and defeated a superior force of the enemy, captured their fieldpiece and about 100 prisoners without losing a man." Six former officers of the 15th Pennsylvania Cavalry had nominated him the previous October to receive the honor, but for the scouting efforts in mufti during the Antietam Campaign that resulted in his capture. The War Department rejected that nomination on the basis that the acts, while valorous, had not been performed of a field of battle. They then submitted a new nomination for the action at Red Hill, which was approved. ==Western railroads==