He continued to lead the regiment during its participation in the battles of Marye's Heights, Salem Church, and Gettysburg. On July 10, 1863, during the Union army's pursuit of the retreating Army of Northern Virginia, Stoughton was severely wounded in an engagement near Funkstown, Maryland, resulting in the loss of his right eye. He resigned on February 2, 1864, as a result of his wounds. In the omnibus promotions that followed the end of the war, he was brevetted a Brigadier General to date from March 13, 1865 in recognition of his faithful and meritorious service.