Schenck was subsequently in command under Maj. Gen. William Rosecrans in West Virginia, and under Maj. Gen. John C. Fremont in the Luray Valley. He took part in the Jackson's Valley Campaign of 1862 in the Shenandoah Valley, the Battle of Cross Keys and was, for a time, commander of the I Corps, in Maj. Gen. Franz Sigel's absence. Ordered to join the Army of Virginia, then under Maj. Gen. John Pope, he joined it just before the Second Battle of Bull Run, and was in the thick of the fighting of the two days that followed, being severely wounded on the second day, and his right arm permanently injured. He was promoted to major general September 18, 1862 to rank from August 30, 1862.