After the start of the Civil War, Wilson received promotions to second and first lieutenant and became the topographical engineer for the Port Royal Expeditionary Force, from September 1861 to March 1862. As the topographical engineer for the Department of the South, he took part in the Battle of Fort Pulaski at the mouth of the Savannah River and received a brevet promotion to major in the regular army for his service. He transferred to the Army of the Potomac in April 1862 and served as its topographic engineer, but also as an aide-de-camp to Maj. Gen. George B. McClellan. He served under McClellan during the Maryland Campaign and was present at the battles of South Mountain and Antietam.