In the fall of 1861, Hobson raised the 13th Kentucky Infantry, and he mustered into the Union army as a colonel in January 1862. His regiment served at Shiloh and throughout the area of Kentucky. However, it was his service at Buffington's Island, Ohio, as a commander that distinguished him. In April 1863, he received the rank of brigadier general. He was captured by the same command which he forced into surrender at Buffington's Island in June 1863. He was paroled and mustered out in August 1865.