When the Civil War broke out, Lane was among the first Texans to call for secession. Lane's military reputation was so great that the first volunteer Confederate company raised in Harrison County was named for him, though Lane would join the 3rd Texas Cavalry. Lane participated in the battles of Wilson's Creek, Missouri, Chustenahlah, Pea Ridge and both the Siege of Corinth and Second Battle of Corinth. Lane led the 3rd Texas at the battle of Franklin, Mississippi, and was commended by General P.G.T. Beauregard for his efforts. Lane was severely wounded in the Battle of Mansfield in 1864, where Confederates forces rebuffed a push to capture either or both Shreveport, Louisiana, or Marshall, Texas. Before the war ended, Lane was promoted to the rank of brigadier general in 1865, being confirmed on the last day the Confederate Congress met.