Morgan was born on March 31, 1831, near Mount Vernon in Fairfax County, Virginia to Mary J. Morgan and her husband Jacob Morgan of Jefferson County. The family moved to Jefferson County in 1837. He was descended from the First Families of Virginia, his great-grandfather Daniel Morgan having famously lead an infantry company from Western Virginia to Boston, Massachusetts in 1775 on what was locally called the "Bee-Line March," to assist patriots during the American Revolutionary War. On December 20, 1854, William A. Morgan married Anna Jaquelin Smith, daughter of Col. Austin C. Smith. They would have at least four sons and three daughters: Augustus C. Morgan, Mary A. Morgan, Bettie M. Morgan, Anna J. Morgan, William A. Morgan and Dr. Daniel Morgan and Archibald M. Morgan.
Career
William A. Morgan led the Shepherdstown cavalry that responded to John Brown's Raid on Harpers Ferry. In July 1861 the company was formally enrolled as Company F of the 1st Virginia Cavalry of the Confederate States Army. It was initially under the command of Col. J. E. B. Stuart with Morgan initially elected as a captain. When Stuart was promoted, Morgan was promoted. He received a commission as Major on October 2, 1862, and his first experience of regimental command after the Battle of Chancellorsville in April 1863. He was promoted to Lt. Colonel on July 16, 1863, then to full colonel on October 21, 1864. His obituary in the Confederate Veteran claimed he was promoted to Brigadier General at war's end. Meanwhile, his wife attempted to run the estate, which was in a contested area, and suffered significant damage during the war. His brother, Daniel H. Morgan, fought with the 6th Sixth Virginia Cavalry until his capture by Union forces and imprisonment at Point Lookout. During the war's final campaign, Morgan had a horse shot out from under him on April 6, 1865 during the Battle of High Bridge. Days later, Morgan and his troops were present at Appomattox Court House but he did not surrender. Morgan laid down his arms in Winchester, Virginia and returned to what was left of his farms in Jefferson County. Resuming farming, Morgan remained active in local civic affairs, becoming the deputy sheriff for Jefferson County in 1872, as well as represented the county at the West Virginia Constitutional Convention that year. He would continue as deputy sheriff for 26 years, until his death. He offered space on his property to the Morgans Grove Agricultural Association, which in 1885 held a very successful fair after the Shenandoah Valley Railroad reached Shepherdstown, and built a stop for the event. The fair continued annually, becoming a four day event, and bought land from Morgan's long-time neighbor, former Confederate delegate and Col. Alexander Boteler in June 1889, then grew more and spilled onto Morgan's property.