In 1861, Hawkins helped raise the 9th New York Infantry, a Zouave-styled regiment, popularly known as "Hawkins Zouaves" for service in the Civil War. Hawkins was appointed colonel of the regiment on May 4, 1861 and served with distinction in North Carolina early in the war. He was part of Benjamin F. Butler's expedition to capture Fort Hatteras in 1861. Expecting to win a promotion to brigadier general for his service at Fort Hatteras he was instead relieved of command for insubordination. On October 8, 1861 a disgruntled Hawkins wrote "brigadier generals are made of such queer stuff nowadays, that I should not esteem it any great honor to be made one." Hawkins would in fact receive a brevet promotion to brigadier general in 1866 to rank from March 13, 1865. Despite his belligerence an early dispatch of Hawkins' caught the attention of President Abraham Lincoln. Hawkins was invited to the White House to confer with the President and General-in-Chief George B. McClellan. There he was instrumental in convincing the Union high command of the possibility of a combined operation against Pamlico Sound in North Carolina.