In early 1861, after receiving a letter from Carter assuring his loyalty to the Union should a civil war break out, Tennessee Governor Andrew Johnson used his influence in the United States Department of War for Carter to organize and train militia within East Tennessee. After leading successful cavalry operations at the Battle of Mill Springs on January 19, 1862, Carter accepted a commission as Brigadier General of volunteers in May and later continued leading operations at the Battle of Cumberland Gap in June as well as raids against Holston, Carter's Station, and Jonesville in December, in support of General William S. Rosecrans' attack on Murfreesboro.