Brown was born in Caldwell County, Kentucky, on 27 May 1817. In March of 1834 be was appointed as a Midshipman in the United States Navy. He was promoted to Lieutenant in 1846. At the outbreak of the American Civil War he resigned his commission. In June 1861 he accepted a commission as Lieutenant in the Confederate States Navy.
Brown was assigned to the Mississippi River region by the Confederate Naval Department. In May of 1862 he was ordered to Yazoo City, Mississippi to take command of the unfinished ironclad CSS Arkansas and complete her construction in the worst of conditions. After successfully accomplishing this difficult task Brown commanded her dramatic breaking of the Federal naval blockade of Vicksburg, Mississippi on 15 July 1862.
Brown was promoted in August 1862 in recognition of his bold and audacious actions at Vicksburg. Commander Brown was named captain of the ironclad CSS Charleston, which operated in defense of Charleston, South Carolina during 1863-1865. At the end of the American Civil War, he took up farming in Mississippi and later moved to Texas. Commander Isaac Newton Brown died at Corsicana, Texas, on 1 September 1889. Brown received the Confederate Medal of Honor for his service.