At the outbreak of the American Civil War, Pennsylvania Governor Andrew Curtin called on Scott for his extensive knowledge of the rail and transportation systems of the state. In May 1861, Scott received a commission as Colonel of Volunteers and placed in command of railroad and telegraph lines used by the Union armies. His friend, Secretary of War Simon Cameron in August 1861 appointed him Assistant Secretary of War, and gave him responsibility for building a railroad through Washington D.C. to connect the Orange and Alexandria Railroad with northern railroads. Scott also advised creating transportation and telegraph bureaus and arranging draft exemptions for experienced civilian mechanics and locomotive engineers, for needed military railroad operations were compromised by the loss of experienced railroad men. The next year, despite Cameron's replacement by Edwin M. Stanton, Scott helped organize the Loyal War Governors' Conference in Altoona, Pennsylvania.