While commanding his artillery battery at the First Battle of Bull Run, Imboden perforated his left eardrum firing an artillery piece, causing subsequent deafness in that ear. He fought with Maj. Gen. Thomas J. "Stonewall" Jackson in the Valley Campaign at Cross Keys and Port Republic. On September 9, 1862, Imboden left the artillery to recruit a battalion of partisan rangers and was promoted to colonel of the 62nd Virginia Mounted Infantry (1st Partisan Rangers). He was promoted to brigadier general on January 28, 1863. Upset by the independence movement in West Virginia, the voters of which petitioned to separate from Virginia, Imboden with Brig. Gen. William E. "Grumble" Jones led 3,400 partisan rangers into northwestern Virginia. The Jones-Imboden Raid destroyed rail track and bridges of the Baltimore and Ohio Railroad, as well as captured thousands of horses and heads of cattle and ruined petroleum fields in the Kanawha Valley. The raiders covered in 37 days but failed to stop West Virginia's statehood. In the Gettysburg Campaign, Imboden's brigade served under Maj. Gen. J.E.B. Stuart guarding the left flank 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 between Martinsburg, West Virginia, and Cumberland, Maryland.) During the Battle of Gettysburg, Imboden's men stayed in the rear and guarded ammunition and supply trains in Chambersburg, Pennsylvania. During the Confederate retreat, Imboden escorted the wagon trains with thousands of wounded soldiers back to Virginia. On July 6, 1863, the Potomac River flooding at Williamsport, Maryland, trapped Imboden's wagon train. 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 Charles Town, West Virginia, on October 18, 1863 at the Battle of Charlestown.