After receiving his commission, RADM Lilly attended the Navy Supply Corps School, Athens, GA.
Upon graduation, he served as Supply & Disbursing Officer of the USS Betelgeuse (AK-260), an attack cargo ship attached to COMSERVLANT, which was used primarily to provide support to the Sixth Fleet in the Mediterranean.
He then served as Disbursing Officer & Assistant to the Supply & Fiscal Officer, NAS Sanford, FL, where he completed his active duty service.
Upon his release from active duty, he joined the Naval Reserve while attending law school. Before his promotion to flag his assignments included Supply Officer, Air Wing Staff79 and. Later NARDIV 791, NAS Memphis, and Commanding Officer, ASB (Advance Supply Base) 109, New Orleans.
His active duty periods in the Naval Reserve included, inter alia, service at Atlantic Fleet Headquarters, Naval Supply Systems Command and Office of the CNO (Logistics).
Following his promotion to Rear Admiral, he served for six years as Commander, Naval Reserve Cargo Handling Force, which included twelve NR Cargo Handling battalions comprising 92 percent of the Navy’s combat stevedores.
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He was awarded the Legion of Merit in 1988 for his leadership of the Cargo Handling Force and Navy Commendation Medal in 1977 for service as Exercise Commander of a National ASB Exercise involving all 18 NR ASB units. RADM Lilly retired from the Naval Reserve in 1988. His retirement ceremony was held in McAlister Auditorium at Tulane, in lieu of the Naval Reserve Center New Orleans, which was under renovation at the time.