Helm was commissioned a colonel on October 19, 1861, and served under Brigadier General Simon B. Buckner in Bowling Green, Kentucky. Helm and the 1st Kentucky were then ordered south. He was promoted to brigadier general on March 14, 1862 and, three weeks later, received a new assignment to raise the 3rd Kentucky Brigade, in the division of Major General John C. Breckinridge. During the Battle of Shiloh, Helm used his brigade to guard the Confederate flanks. In 1862, he was also sent to protect the "Arkansas", an ironclad warship of the Confederate Navy under construction in Yazoo City, Mississippi. Serving under Breckinridge in January 1863, he was given command of the First Kentucky Brigade, commonly known as the ""Orphan Brigade"". Helm's brigade was assigned to the Army of Tennessee, where it participated in the 1863 Tullahoma and Chickamauga campaigns. Near the end of the spring of 1863, Breckinridge ordered Helm to deploy the brigade to Vicksburg, Mississippi to participate in General Joseph E. Johnston's unsuccessful attempt to break the siege. Helm called it "the most unpleasant and trying [campaign] of his career".