Leading a brigade at the Battle of Fredericksburg, Cooke was badly wounded by a bullet which fractured his skull. He was able to return to the field in April 1863. In October 1863, while commanding a brigade in A.P. Hill's corps, Cooke received another serious wound at the Battle of Bristoe Station during Hill's attack on the Union II Corps. His shattered shinbone took months to heal, and during his recovery Cooke served on military tribunal in Richmond. Upon returning to field duty, Cooke received another leg wound during the Battle of Spotsylvania, but remained on the field to lead an assault from horseback. In all, Cooke was wounded seven times during the Civil War. Cooke's brigade played a significant role in the Battle of Sutherland's Station, its resistance to Union attacks enabling other Confederate units to retreat.