On July 1, 1861, the Staunton Light Artillery, with its four bronze, 6-pounder guns and 107 officers and men, was formally mustered in the Confederate States Army. 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.