In January 1861, Brown was appointed military commander of
Washington, D.C., and
Fort McHenry and remained in this capacity until war broke out four months later. He was initially assigned to the 4th United States Artillery but, declining promotion to
brigadier general, he was appointed commanding officer of the new 5th United States Artillery on May 14, 1861. Placed in command of the expedition to hold
Fort Pickens in
Confederate held Florida, he
successfully defended Santa Rosa Island on October 9 On April 25, 1862,
President Abraham Lincoln nominated Brown for appointment to the grade of
brevet brigadier general in the
regular army, to rank from November 23, 1861, for "gallantry and good conduct during the engagement of November 22 and 23, 1861 between Fort Pickens and the rebel batteries", and the
United States Senate confirmed the appointment on March May 12, 1862. Brown was appointed commander of
New York Harbor in April 1862 and full military commander in January 1863. He remained in New York for over a year and, during the
New York Draft Riots, Brown oversaw military operations against the rioters and was especially involved in the final suppression of the rioters. He retired from active duty on August 1, 1863. On December 11, 1866,
President Andrew Johnson nominated Brown for appointment to the grade of brevet
major general in the regular army, to rank from August 2, 1866, and the
United States Senate confirmed the appointment on February 23, 1867 (recalled February 25 and reconfirmed March 2, 1867). ==Postbellum life==