In January 1944, he entered the Army Specialized Training Program to attend the University of Kansas where he hoped to become a civil engineer.

In August 1944, he was sent to basic training at Camp Fannin, Texas, and then to Officer Candidate School at Fort Benning, Georgia.

In 1961, he was assigned to an overseas replacement battle group and transferred to the Seventh Infantry Division in Korea From 1962 to 1966, he served on the staff of the US Army Chaplain School, Fort Hamilton, New York.

On April 7, 1975, Reverend Kelly was nominated by President Ford for the appointment as Chief of Chaplains, Department of the Army, with promotion from lieutenant colonel to major general.

The Senate confirmed the nomination on April 29, 1975, and promotion ceremonies were conducted on August 1, 1975, by General Walter T. Kerwin, Jr., Vice Chief of Staff of the United States Army.

On August 1, 1979, he assumed the position of Associate General Secretary for the Division of Chaplains and Related Ministries (DCRM).