Along with Brig. Gen. William E. "Grumble" Jones, Imboden led the famous Jones-Imboden raid of 3,400 troopers into northwestern Virginia against the B & O Railroad, destroying rail track and bridges. During the raid he also captured thousands of horses and heads of cattle and ruined the petroleum fields in the Kanawha Valley. This raid covered in 37 days. In the Gettysburg Campaign, Imboden's brigade served under Maj. Gen. J.E.B. Stuart as the rearguard for Gen. Robert E. Lee's movement north through the Shenandoah Valley. (His brigade did not participate in Stuart's foray away from Lee's army, but instead raided the Baltimore and Ohio Railroad in Bedford County, Pennsylvania.) They spent the Battle of Gettysburg guarding ammunition and supply trains in Chambersburg, Pennsylvania. During the Confederate retreat, Imboden was in charge of escorting the wagon trains of thousands of wounded soldiers back to Virginia. On July 6, 1863, the Potomac River was flooding at Williamsport, Maryland, and Imboden's wagon train was trapped. He put together a defensive force that included an artillery battery and as many of the wounded who could operate muskets. This hastily organized force turned back attacks from Union cavalry generals John Buford and Judson Kilpatrick, saving the wagon train. Robert E. Lee praised Imboden for the way in which he "gallantly repulsed" the Union cavalry.
Returning to the Shenandoah Valley, Imboden responded to a request from General Lee to distract the enemy in his front by leading a raid on the vulnerable Union detachment at Charlestown, West Virginia, on October 18, 1863 at the Battle of Charlestown. Imboden reported, Union Brig. Gen. Jeremiah Cutler Sullivan soon sent a rescue column from nearby Harpers Ferry and drove Imboden back up the valley. Sullivan reported, "The cavalry came up with the enemy this side of Charlestown, and drove them through the town. Artillery coming up, drove them about 4 miles. A portion of infantry force..., reaching them, the enemy were driven from every position they took, to near Berryville."
Imboden and John C. Breckinridge's forces defeated Union Maj. Gen. Franz Sigel's command at the Battle of New Market on May 15, 1864. He returned to Virginia and commanded a brigade in Maj. Gen. Robert Ransom's cavalry division of the Second Corps of the Army of Northern Virginia under Lt. Gen. Jubal A. Early in the Valley Campaigns of 1864. He was incapacitated by typhoid fever and left the active cavalry service.
Beginning on January 2, 1865, Imboden commanded Camp Millen, Georgia, then the prison camp at Aiken, South Carolina as well as other prison camps in Georgia, Alabama, and Mississippi throughout 1865 until the end of the war. He was paroled in Augusta, Georgia on May 3 of that year.