In 1861, Drake raised a company for the 2nd Iowa Infantry, in defense of his home state. In August 1862, Drake received a commission as a lieutenant colonel in the Thirty-sixth Iowa Infantry. In April 1864, he commanded forces at the Battle of Elkins' Ford. On April 25th, he attempted to command forces against a larger Union force at Marks' Mill, Arkansas, which resulted in a Confederate victory. Drake was severely wounded in this action. He would return to service shortly before the end of the war. He was brevetted the rank of brigadier general.