He hid out with his Howard County relatives while recuperating. When he recovered, he resumed his recruiting activities and, with a small band of partisans, remained in Missouri. On January 11, 1863, Jackman's band raided Columbia, Missouri, in an unsuccessful attempt to release comrades from the town jail. On April 23, 1863, Jackman kidnapped Brigadier General Thomas J. Bartholow, then encamped at Glasgow, Missouri, in circumstances reminiscent of John S. Mosby's famous capture of General Stoughton. On June 1, 1863, Jackman's twenty-man band beat off an attack by picked Union cavalry; Jackman personally shot the major who led the Union forces. By May, 1864, Jackman and his men crossed over into Arkansas. He hid out in the Boston Mountains of northwest Arkansas, skirmishing with the Union army occupation forces and organizing recruits. By June he succeeded in raising a cavalry regiment that was called "Jackman's Missouri Cavalry."

The regiment was attached to Brigadier General Joseph Shelby's cavalry division. In the fall of 1864 Jackman, "a stern, able and devoted soldier,"' commanded as colonel a brigade of Missouri cavalry (two regiments and two battalions of mostly new recruits) in Price's Raid. During the raid Jackman led the attack and capture of Glasgow, Missouri, and its Union garrison. On the first day of the Battle of Westport (October 22 and 23, 1864), Jackman led the attack of Price's army, routing the Union forces from their position. On the second day Jackman's brigade, on the Confederate left, launched a successful attack on Westport. With the collapse of the Confederate rear the attack was halted, and Jackman's brigade was hustled back to hold off the Union pursuit. At Mine Creek Jackman's troopers guarded the army's trains and thus missed the rout, though the brigade did help blunt the Union pursuit. Jackman was twice wounded during the war.

On May 16, 1865, General Kirby Smith assigned Jackman to duty as brigadier general. The assignment orders list him as Colonel of Jackman's Missouri Cavalry. At this stage of the war the soldiers of the Trans-Mississippi army, hearing that Lee had surrendered and believing that the war was lost, were deserting in droves; the army soon ceased to exist.

After the surrender of the Trans-Mississippi Department, Jackman gathered his family and headed for Mexico. He left his family in Hays County, Texas, while he went ahead to gauge the prospects of settling in northern Mexico. In 1866 he rejoined his family in Hays County. Settling near Kyle, he bought a farm and became a farmer and cattle raiser. Respected in his new community, Jackman was elected representative to the Texas Legislature in 1873. In 1885, President Cleveland appointed Jackman U.S. marshal for western Texas. He served as marshal until his death, passing away on June 2, 1886, at his Hays County ranch. He is buried in Kyle Cemetery in Hays County. It was said of Jackman that "truth, honor and duty constituted his life-creed"; he was profoundly loyal to friends, family and country."'