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."[2] 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.[3]
The idea became the objective of Ambrose Burnside's North Carolina Expedition. Hawkins was again conspicuous at the battles of Roanoke Island and New Bern in 1862. Upon the arrival of significant reinforcements to North Carolina in April 1862, he assumed command of a brigade. Hawkins' brigade was attached to Jesse L. Reno's division and fought at the Battle of South Mills on April 19, 1862, where he was wounded in the left arm.[4]
After recovering Hawkins returned to Virginia with his regiment and briefly commanded the 1st Brigade, 3rd Division in the newly formed IX Corps. He was not present with the brigade during the Maryland Campaign but resumed command during the battle of Fredericksburg. After Fredericksburg, the 3rd Division, commanded by George W. Getty, was transferred to the VII Corps in southeast Virginia. Hawkins led his brigade (now the 1st Brigade, 2nd Division, VII Corps) during the siege of Suffolk. Just two days before the siege was lifted, Hawkins turned over command of his brigade and on May 20, 1863, was mustered out of the volunteer service with his old regiment.[4] He did not return to active duty. On July 9, 1866, President Andrew Johnson nominated Hawkins for appointment to the grade of brevet brigadier general of volunteers, to rank from March 13, 1865, and the United States Senate confirmed the appointment on July 23, 1866.[5] He remained active in the New York Militia receiving a brevet promotion to brigadier general of New York Militia in 1865.[4]