Lane joined the Confederate Army and was commissioned as a major in the 1st North Carolina Volunteers on May 11, 1861. He participated in the Battle of Big Bethel and was made lieutenant colonel. Further promotion came quickly and he was a colonel and commander of the 28th North Carolina Infantry Regiment by September 15. In the Seven Days Battles of 1862 he was twice wounded leading his regiment. He served in Major General A.P. Hill's division of Thomas J. "Stonewall" Jackson's Second Corps for Second Bull Run and took over brigade command following the death of Brigadier General Lawrence O. Branch at the Battle of Antietam. He was promoted to brigadier general on November 1, 1862. It was soldiers with Major John D. Barry of Lane's brigade that accidentally shot General Jackson as he returned from a nighttime scouting trip in front of the Confederate lines during the Battle of Chancellorsville. Lane's command became the 2nd Brigade in W. Dorsey Pender's division of Hill's Third Corps of the Army of Northern Virginia the following May, directly before the beginning of the Gettysburg Campaign.